Merge branch 'non-umi' into dev (40bda015) · Commits · github_fork / Universc

CHANGELOG

+3 −1

Original line number	Original line	Diff line number	Diff line
	@@ -8,7 +8,9 @@

	- add full support for dual indexes (e.g., inDrops v3, SCI-RNA-Seq, Smart-Seq3)		- add full support for dual indexes (e.g., inDrops v3, SCI-RNA-Seq, Smart-Seq3)

	- compatilibility with counting reads for non-UMI technologies (e.g., Smart-Seq2)		- compatilibility with counting reads for non-UMI technologies (e.g., ICELL8-v2, Quartz-Seq, RamDA-Seq, Smart-Seq2, STRT-Seq)

			- implements option to replace UMI with mock UMI to force counting reads only

	- support custom whitelists from mixed samples with a low fraction of reads		- support custom whitelists from mixed samples with a low fraction of reads

README.Rmd

+33 −24

Original line number	Original line	Diff line number	Diff line
	@@ -168,7 +168,9 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
	- CEL-Seq		- CEL-Seq
	- CEL-Seq (8 bp barcode, 4 bp UMI): celseq		- CEL-Seq (8 bp barcode, 4 bp UMI): celseq
	- CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2		- CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2
	- Drop-Seq (12 bp barcode, 8 bp UMI): nadia, dropseq		- Drop-Seq (12 bp barcode, 8 bp UMI): dropseq
			- ICELL8
			- ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2
	- ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom		- ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom
	- inDrops		- inDrops
	- inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1		- inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1
	@@ -178,10 +180,13 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
	- MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1		- MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1
	- MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2		- MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
	- Microwell-Seq (18 bp barcode, 6 bp UMI): microwell		- Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
			- Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq
	- Quartz-Seq		- Quartz-Seq
			- QuartzSeq (6 bp index, no UMI): quartz-seq
	- Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384		- Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
	- Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536		- Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536
	- Single-cell combinatorial indexing		- RamDA-Seq (6 bp index, no UMI): ramda-seq
			- Single-cell combinatorial indexing (SCI-RNA-Seq)
	- SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2		- SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
	- SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3		- SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
	- SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq		- SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq
	@@ -189,8 +194,9 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
	- SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3		- SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3
	- SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq		- SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq
	- Smart-seq		- Smart-seq
	- Smart-seq2 (16 bp barcode, No UMI): smartseq2		- Smart-Seq (16 bp barcode, No UMI): smartseq
	- Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3		- Smart-Seq2 (16 bp barcode, No UMI): smartseq2
			- Smart-Seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3
	- STRT-Seq		- STRT-Seq
	- STRT-Seq (6 bp barcode, no UMI)		- STRT-Seq (6 bp barcode, no UMI)
	- STRT-Seq-C1 (8 bp barode, 5 bp UMI)		- STRT-Seq-C1 (8 bp barode, 5 bp UMI)
	@@ -199,17 +205,17 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De

	All technologies support 3' single-cell RNA-Seq. Barcode adjustments and		All technologies support 3' single-cell RNA-Seq. Barcode adjustments and
	whitelists are changed automatically. For 5' single-cell RNA-Seq, this		whitelists are changed automatically. For 5' single-cell RNA-Seq, this
	is only supported for 10x Genomics version 2 chemistry. This is detected		is only supported for 10x Genomics version 2 chemistry, ICELL8,
	automatically but can be configured with the `--chemistry` argument.		Smart-Seq, and STRT-Seq.
			For 10x Genomics, this is detected automatically but can be
	We are developing technologies to support dual indexes and full length scRNA kits.		configured with the `--chemistry` argument.
			For other technologies, the template switching oligonucleotide
	Experimental technologies (not yet supported):		is automatically converted to the match the 10x sequence.
	- ICELL8 (11 bp barcode, no UMI)
	- RamDA-Seq (6 bp index, no UMI)		Single indexes are supported for STRT-Seq, Quartz-Seq, and RamDA-Seq.
	- QuartzSeq (6 bp index, no UMI)		Dual indexes are supported for inDrops-v3, SCI-RNA-Seq, scifi-seq, and Smart-Seq.
	- SmartSeq2 (16 bp barcode, no UMI)		Combinatorial indexing technologies have linkers between barcodes removed
			automatically to match the barcode whitelist.

	#### Dual-indexing		#### Dual-indexing

	@@ -232,6 +238,10 @@ Custom inputs are also supported by giving the name "custom" and length of barco
	Custom barcode files are also supported for preset technologies. These are particularly useful for well-based		Custom barcode files are also supported for preset technologies. These are particularly useful for well-based
	technologies to demutliplex based on the wells.		technologies to demutliplex based on the wells.

			Note that custom inputs do not remove linker or adapter sequences for combinatorial indexng technologies.
			These must be removed from the Read 1 file before running UniverSC. To request a preset technology
			setting instead, please submit a feature request on GitHub as described below.

	## Release		## Release

	This tool will be released open-source (see [legal stuff](#licensing) below).		This tool will be released open-source (see [legal stuff](#licensing) below).
	@@ -1012,22 +1022,27 @@ Mandatory arguments to long options are mandatory for short options too.
	BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody		BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody
	CEL-Seq (8 bp barcode, 4 bp UMI): celseq		CEL-Seq (8 bp barcode, 4 bp UMI): celseq
	CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2		CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2
	Drop-Seq (12 bp barcode, 8 bp UMI): nadia, dropseq		Drop-Seq (12 bp barcode, 8 bp UMI): dropseq
			ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2
	ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom		ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom
	inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1		inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1
	inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2		inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2
	inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3		inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3
			Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq
	MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1		MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1
	MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2		MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
	Microwell-Seq (18 bp barcode, 6 bp UMI): microwell		Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
			QuartzSeq (6 bp index, no UMI): quartz-seq
	Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384		Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
	Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536		Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536
			RamDA-Seq (6 bp index, no UMI): ramda-seq
	SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2		SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
	SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3		SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
	SCIFI-Seq (27 bp barcode, 8 bp UMI		SCIFI-Seq (27 bp barcode, 8 bp UMI
	SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq		SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq
	SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3		SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3
	Smart-seq, Smart-seq2 (16 bp barcode, No UMI): smartseq2		Smart-seq (16 bp barcode, No UMI): smartseq
			Smart-seq2 (16 bp barcode, No UMI): smartseq2
	Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3		Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3
	SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq		SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq
	STRT-Seq (6 bp barcode, no UMI)		STRT-Seq (6 bp barcode, no UMI)
	@@ -1037,12 +1052,6 @@ Mandatory arguments to long options are mandatory for short options too.
	Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
	e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10		e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10

	Experimental
	ICELL8 (11 bp barcode, no UMI)
	RamDA-Seq (6 bp index, no UMI)
	QuartzSeq (6 bp index, no UMI)
	SmartSeq2 (16 bp barcode, no UMI)

	-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)

	-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: SC3Pv2 (default), SC5P-PE, or SC5P-R2		-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: SC3Pv2 (default), SC5P-PE, or SC5P-R2

README.html

+22 −15

Original line number	Original line	Diff line number	Diff line
	@@ -52,8 +52,12 @@
	<li>CEL-Seq (8 bp barcode, 4 bp UMI): celseq</li>		<li>CEL-Seq (8 bp barcode, 4 bp UMI): celseq</li>
	<li>CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2</li>		<li>CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2</li>
	</ul></li>		</ul></li>
	<li>Drop-Seq (12 bp barcode, 8 bp UMI): nadia, dropseq</li>		<li>Drop-Seq (12 bp barcode, 8 bp UMI): dropseq</li>
			<li>ICELL8
			<ul>
			<li>ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2</li>
	<li>ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom</li>		<li>ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom</li>
			</ul></li>
	<li>inDrops		<li>inDrops
	<ul>		<ul>
	<li>inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1</li>		<li>inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1</li>
	@@ -67,12 +71,15 @@
	</li>		</li>
	</ul></li>		</ul></li>
	<li>Microwell-Seq (18 bp barcode, 6 bp UMI): microwell</li>		<li>Microwell-Seq (18 bp barcode, 6 bp UMI): microwell</li>
			<li>Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq</li>
	<li>Quartz-Seq		<li>Quartz-Seq
	<ul>		<ul>
			<li>QuartzSeq (6 bp index, no UMI): quartz-seq</li>
	<li>Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384</li>		<li>Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384</li>
	<li>Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536</li>		<li>Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536</li>
	</ul></li>		</ul></li>
	<li>Single-cell combinatorial indexing</li>		<li>RamDA-Seq (6 bp index, no UMI): ramda-seq</li>
			<li>Single-cell combinatorial indexing (SCI-RNA-Seq)</li>
	<li>SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2</li>		<li>SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2</li>
	<li>SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3</li>		<li>SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3</li>
	<li>SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq</li>		<li>SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq</li>
	@@ -80,8 +87,9 @@
	<li>SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3</li>		<li>SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3</li>
	<li>SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq</li>		<li>SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq</li>
	<li>Smart-seq</li>		<li>Smart-seq</li>
	<li>Smart-seq2 (16 bp barcode, No UMI): smartseq2</li>		<li>Smart-Seq (16 bp barcode, No UMI): smartseq</li>
	<li>Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3</li>		<li>Smart-Seq2 (16 bp barcode, No UMI): smartseq2</li>
			<li>Smart-Seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3</li>
	<li>STRT-Seq		<li>STRT-Seq
	<ul>		<ul>
	<li>STRT-Seq (6 bp barcode, no UMI)</li>		<li>STRT-Seq (6 bp barcode, no UMI)</li>
	@@ -90,9 +98,8 @@
	</ul></li>		</ul></li>
	<li>SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad</li>		<li>SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad</li>
	</ul>		</ul>
	<p>All technologies support 3' single-cell RNA-Seq. Barcode adjustments and whitelists are changed automatically. For 5' single-cell RNA-Seq, this is only supported for 10x Genomics version 2 chemistry. This is detected automatically but can be configured with the <code>--chemistry</code> argument.</p>		<p>All technologies support 3' single-cell RNA-Seq. Barcode adjustments and whitelists are changed automatically. For 5' single-cell RNA-Seq, this is only supported for 10x Genomics version 2 chemistry, ICELL8, Smart-Seq, and STRT-Seq. For 10x Genomics, this is detected automatically but can be configured with the <code>--chemistry</code> argument. For other technologies, the template switching oligonucleotide is automatically converted to the match the 10x sequence.</p>
	<p>We are developing technologies to support dual indexes and full length scRNA kits.</p>		<p>Single indexes are supported for STRT-Seq, Quartz-Seq, and RamDA-Seq. Dual indexes are supported for inDrops-v3, SCI-RNA-Seq, scifi-seq, and Smart-Seq. Combinatorial indexing technologies have linkers between barcodes removed automatically to match the barcode whitelist.</p>
	<p>Experimental technologies (not yet supported): - ICELL8 (11 bp barcode, no UMI) - RamDA-Seq (6 bp index, no UMI) - QuartzSeq (6 bp index, no UMI) - SmartSeq2 (16 bp barcode, no UMI)</p>
	<h4 id="dual-indexing">Dual-indexing</h4>		<h4 id="dual-indexing">Dual-indexing</h4>
	<p>For dual-indexed technologies such as inDrops-v3, Sci-Seq, SmartSeq3 it is advised to use "bcl2fastq" before calling UniverSC:</p>		<p>For dual-indexed technologies such as inDrops-v3, Sci-Seq, SmartSeq3 it is advised to use "bcl2fastq" before calling UniverSC:</p>
	<pre><code> /usr/local/bin/bcl2fastq -v --runfolder-dir "/path/to/illumina/bcls" --output-dir "./Data/Intensities/BaseCalls"\		<pre><code> /usr/local/bin/bcl2fastq -v --runfolder-dir "/path/to/illumina/bcls" --output-dir "./Data/Intensities/BaseCalls"\
	@@ -103,6 +110,7 @@
	<p>Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by a "_" character.</p>		<p>Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by a "_" character.</p>
	<p>e.g. Custom (16bp barcode, 10bp UMI): <code>custom_16_10</code></p>		<p>e.g. Custom (16bp barcode, 10bp UMI): <code>custom_16_10</code></p>
	<p>Custom barcode files are also supported for preset technologies. These are particularly useful for well-based technologies to demutliplex based on the wells.</p>		<p>Custom barcode files are also supported for preset technologies. These are particularly useful for well-based technologies to demutliplex based on the wells.</p>
			<p>Note that custom inputs do not remove linker or adapter sequences for combinatorial indexng technologies. These must be removed from the Read 1 file before running UniverSC. To request a preset technology setting instead, please submit a feature request on GitHub as described below.</p>
	<h2 id="release">Release</h2>		<h2 id="release">Release</h2>
	<p>This tool will be released open-source (see <a href="#licensing">legal stuff</a> below). We welcome any feedback on it and any contributions to improve it. Hopefully it will save people time by making it easier to compare technologies.</p>		<p>This tool will be released open-source (see <a href="#licensing">legal stuff</a> below). We welcome any feedback on it and any contributions to improve it. Hopefully it will save people time by making it easier to compare technologies.</p>
	<p>We have tested it on several technologies but we need users like you to let us know how we can improve it. We hope that it will save you time by handing tedious parts of data formatting so that you can focus on the results.</p>		<p>We have tested it on several technologies but we need users like you to let us know how we can improve it. We hope that it will save you time by handing tedious parts of data formatting so that you can focus on the results.</p>
	@@ -495,22 +503,27 @@ Mandatory arguments to long options are mandatory for short options too.
	BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody		BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody
	CEL-Seq (8 bp barcode, 4 bp UMI): celseq		CEL-Seq (8 bp barcode, 4 bp UMI): celseq
	CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2		CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2
	Drop-Seq (12 bp barcode, 8 bp UMI): nadia, dropseq		Drop-Seq (12 bp barcode, 8 bp UMI): dropseq
			ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2
	ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom		ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom
	inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1		inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1
	inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2		inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2
	inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3		inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3
			Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq
	MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1		MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1
	MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2		MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
	Microwell-Seq (18 bp barcode, 6 bp UMI): microwell		Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
			QuartzSeq (6 bp index, no UMI): quartz-seq
	Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384		Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
	Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536		Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536
			RamDA-Seq (6 bp index, no UMI): ramda-seq
	SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2		SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
	SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3		SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
	SCIFI-Seq (27 bp barcode, 8 bp UMI		SCIFI-Seq (27 bp barcode, 8 bp UMI
	SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq		SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq
	SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3		SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3
	Smart-seq, Smart-seq2 (16 bp barcode, No UMI): smartseq2		Smart-seq (16 bp barcode, No UMI): smartseq
			Smart-seq2 (16 bp barcode, No UMI): smartseq2
	Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3		Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3
	SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq		SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq
	STRT-Seq (6 bp barcode, no UMI)		STRT-Seq (6 bp barcode, no UMI)
	@@ -520,12 +533,6 @@ Mandatory arguments to long options are mandatory for short options too.
	Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
	e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10		e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10

	Experimental
	ICELL8 (11 bp barcode, no UMI)
	RamDA-Seq (6 bp index, no UMI)
	QuartzSeq (6 bp index, no UMI)
	SmartSeq2 (16 bp barcode, no UMI)

	-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)

	-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: SC3Pv2 (default), SC5P-PE, or SC5P-R2		-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: SC3Pv2 (default), SC5P-PE, or SC5P-R2

README.md

+33 −24

Original line number	Original line	Diff line number	Diff line
	@@ -168,7 +168,9 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
	- CEL-Seq		- CEL-Seq
	- CEL-Seq (8 bp barcode, 4 bp UMI): celseq		- CEL-Seq (8 bp barcode, 4 bp UMI): celseq
	- CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2		- CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2
	- Drop-Seq (12 bp barcode, 8 bp UMI): nadia, dropseq		- Drop-Seq (12 bp barcode, 8 bp UMI): dropseq
			- ICELL8
			- ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2
	- ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom		- ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom
	- inDrops		- inDrops
	- inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1		- inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1
	@@ -178,10 +180,13 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
	- MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1		- MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1
	- MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2		- MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
	- Microwell-Seq (18 bp barcode, 6 bp UMI): microwell		- Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
			- Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq
	- Quartz-Seq		- Quartz-Seq
			- QuartzSeq (6 bp index, no UMI): quartz-seq
	- Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384		- Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
	- Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536		- Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536
	- Single-cell combinatorial indexing		- RamDA-Seq (6 bp index, no UMI): ramda-seq
			- Single-cell combinatorial indexing (SCI-RNA-Seq)
	- SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2		- SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
	- SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3		- SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
	- SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq		- SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq
	@@ -189,8 +194,9 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
	- SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3		- SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3
	- SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq		- SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq
	- Smart-seq		- Smart-seq
	- Smart-seq2 (16 bp barcode, No UMI): smartseq2		- Smart-Seq (16 bp barcode, No UMI): smartseq
	- Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3		- Smart-Seq2 (16 bp barcode, No UMI): smartseq2
			- Smart-Seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3
	- STRT-Seq		- STRT-Seq
	- STRT-Seq (6 bp barcode, no UMI)		- STRT-Seq (6 bp barcode, no UMI)
	- STRT-Seq-C1 (8 bp barode, 5 bp UMI)		- STRT-Seq-C1 (8 bp barode, 5 bp UMI)
	@@ -199,17 +205,17 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De

	All technologies support 3' single-cell RNA-Seq. Barcode adjustments and		All technologies support 3' single-cell RNA-Seq. Barcode adjustments and
	whitelists are changed automatically. For 5' single-cell RNA-Seq, this		whitelists are changed automatically. For 5' single-cell RNA-Seq, this
	is only supported for 10x Genomics version 2 chemistry. This is detected		is only supported for 10x Genomics version 2 chemistry, ICELL8,
	automatically but can be configured with the `--chemistry` argument.		Smart-Seq, and STRT-Seq.
			For 10x Genomics, this is detected automatically but can be
	We are developing technologies to support dual indexes and full length scRNA kits.		configured with the `--chemistry` argument.
			For other technologies, the template switching oligonucleotide
	Experimental technologies (not yet supported):		is automatically converted to the match the 10x sequence.
	- ICELL8 (11 bp barcode, no UMI)
	- RamDA-Seq (6 bp index, no UMI)		Single indexes are supported for STRT-Seq, Quartz-Seq, and RamDA-Seq.
	- QuartzSeq (6 bp index, no UMI)		Dual indexes are supported for inDrops-v3, SCI-RNA-Seq, scifi-seq, and Smart-Seq.
	- SmartSeq2 (16 bp barcode, no UMI)		Combinatorial indexing technologies have linkers between barcodes removed
			automatically to match the barcode whitelist.

	#### Dual-indexing		#### Dual-indexing

	@@ -232,6 +238,10 @@ Custom inputs are also supported by giving the name "custom" and length of barco
	Custom barcode files are also supported for preset technologies. These are particularly useful for well-based		Custom barcode files are also supported for preset technologies. These are particularly useful for well-based
	technologies to demutliplex based on the wells.		technologies to demutliplex based on the wells.

			Note that custom inputs do not remove linker or adapter sequences for combinatorial indexng technologies.
			These must be removed from the Read 1 file before running UniverSC. To request a preset technology
			setting instead, please submit a feature request on GitHub as described below.

	## Release		## Release

	This tool will be released open-source (see [legal stuff](#licensing) below).		This tool will be released open-source (see [legal stuff](#licensing) below).
	@@ -1012,22 +1022,27 @@ Mandatory arguments to long options are mandatory for short options too.
	BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody		BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody
	CEL-Seq (8 bp barcode, 4 bp UMI): celseq		CEL-Seq (8 bp barcode, 4 bp UMI): celseq
	CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2		CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2
	Drop-Seq (12 bp barcode, 8 bp UMI): nadia, dropseq		Drop-Seq (12 bp barcode, 8 bp UMI): dropseq
			ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2
	ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom		ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom
	inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1		inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1
	inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2		inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2
	inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3		inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3
			Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq
	MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1		MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1
	MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2		MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
	Microwell-Seq (18 bp barcode, 6 bp UMI): microwell		Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
			QuartzSeq (6 bp index, no UMI): quartz-seq
	Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384		Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
	Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536		Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536
			RamDA-Seq (6 bp index, no UMI): ramda-seq
	SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2		SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
	SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3		SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
	SCIFI-Seq (27 bp barcode, 8 bp UMI		SCIFI-Seq (27 bp barcode, 8 bp UMI
	SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq		SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq
	SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3		SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3
	Smart-seq, Smart-seq2 (16 bp barcode, No UMI): smartseq2		Smart-seq (16 bp barcode, No UMI): smartseq
			Smart-seq2 (16 bp barcode, No UMI): smartseq2
	Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3		Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3
	SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq		SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq
	STRT-Seq (6 bp barcode, no UMI)		STRT-Seq (6 bp barcode, no UMI)
	@@ -1037,12 +1052,6 @@ Mandatory arguments to long options are mandatory for short options too.
	Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
	e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10		e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10

	Experimental
	ICELL8 (11 bp barcode, no UMI)
	RamDA-Seq (6 bp index, no UMI)
	QuartzSeq (6 bp index, no UMI)
	SmartSeq2 (16 bp barcode, no UMI)

	-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)

	-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: SC3Pv2 (default), SC5P-PE, or SC5P-R2		-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: SC3Pv2 (default), SC5P-PE, or SC5P-R2

launch_universc.sh

+197 −23

File changed.

Preview size limit exceeded, changes collapsed.

Admin message