update documentation with subheadings

    -  STRT-Seq-2i (13 bp barcode, 6 bp UMI)

-  SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad

All technologies support 3' single-cell RNA-Seq. Barcode adjustments and

whitelists are changed automatically. For 5' single-cell RNA-Seq, this

#### Chemistry settings available

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

For other technologies, the template switching oligonucleotide

is automatically converted to the match the 10x sequence. 

#### Support for UMI-based and non-UMI technologies 

By default, UMIs are supported where available so with the following

exceptions for non-UMI technologies:

ICELL8 v2, RamDA-Seq, Quartz-Seq, Smart-Seq, Smart-Seq2.

While using UMI is recommended we provide a mock UMI for counting

reads for these technologies (and data from previous versions).

Other techniques can be forced to replace the UMI with a mock sequence

for counting reads only with `--non-umi` or `--read-only` arguments.

Forcing non-UMI techniques is _not recommended_ unless you are 

non-UMI (icell8-v2, smartseq2) and UMI-based (icell8-v3, smartseq3)

techniques are available it is possible to specify which to use.

#### Single and dual indexed technologies

Where needed the cell barcode can be detected in the index I1 or I2 file.

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

</ul></li>

<li>SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad</li>

</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, 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>By default, UMIs are supported where available so with the following exceptions for non-UMI technologies: ICELL8 v2, RamDA-Seq, Quartz-Seq, Smart-Seq, Smart-Seq2. Other techniques can be forced to replace the UMI with a mock sequence for counting reads only with <code>--non-umi</code> or <code>--read-only</code> arguments. Forcing non-UMI techniques is <em>not recommended</em> unless you are integrating non-UMI and UMI-based technologies. It is not necessary to specific <code>--non-umi</code> for non-UMI techniques as these will be used automatically when applicable. For ICELL8 and Smart-Seq where both non-UMI (icell8-v2, smartseq2) and UMI-based (icell8-v3, smartseq3) techniques are available it is possible to specify which to use.</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>

<h4 id="chemistry-settings-available">Chemistry settings available</h4>

<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>

<h4 id="support-for-umi-based-and-non-umi-technologies">Support for UMI-based and non-UMI technologies</h4>

<p>By default, UMIs are supported where available so with the following exceptions for non-UMI technologies: ICELL8 v2, RamDA-Seq, Quartz-Seq, Smart-Seq, Smart-Seq2. While using UMI is recommended we provide a mock UMI for counting reads for these technologies (and data from previous versions).</p>

<p>Other techniques can be forced to replace the UMI with a mock sequence for counting reads only with <code>--non-umi</code> or <code>--read-only</code> arguments. Forcing non-UMI techniques is <em>not recommended</em> unless you are integrating non-UMI and UMI-based technologies. It is not necessary to specific <code>--non-umi</code> for non-UMI techniques as these will be used automatically when applicable. For ICELL8 and Smart-Seq where both non-UMI (icell8-v2, smartseq2) and UMI-based (icell8-v3, smartseq3) techniques are available it is possible to specify which to use.</p>

<h4 id="single-and-dual-indexed-technologies">Single and dual indexed technologies</h4>

<p>Where needed the cell barcode can be detected in the index I1 or I2 file. 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>

<h4 id="demultiplexing-for-dual-indexing">Demultiplexing for dual-indexing</h4>

<p>For dual-indexed technologies such as inDrops-v3, Sci-Seq, SmartSeq3 it is advised to use &quot;bcl2fastq&quot; before calling UniverSC:</p>

<pre><code>   /usr/local/bin/bcl2fastq  -v --runfolder-dir &quot;/path/to/illumina/bcls&quot;  --output-dir &quot;./Data/Intensities/BaseCalls&quot;\

    -  STRT-Seq-2i (13 bp barcode, 6 bp UMI)

-  SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad

All technologies support 3' single-cell RNA-Seq. Barcode adjustments and

whitelists are changed automatically. For 5' single-cell RNA-Seq, this

#### Chemistry settings available

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

For other technologies, the template switching oligonucleotide

is automatically converted to the match the 10x sequence. 

#### Support for UMI-based and non-UMI technologies 

By default, UMIs are supported where available so with the following

exceptions for non-UMI technologies:

ICELL8 v2, RamDA-Seq, Quartz-Seq, Smart-Seq, Smart-Seq2.

While using UMI is recommended we provide a mock UMI for counting

reads for these technologies (and data from previous versions).

Other techniques can be forced to replace the UMI with a mock sequence

for counting reads only with `--non-umi` or `--read-only` arguments.

Forcing non-UMI techniques is _not recommended_ unless you are 

non-UMI (icell8-v2, smartseq2) and UMI-based (icell8-v3, smartseq3)

techniques are available it is possible to specify which to use.

#### Single and dual indexed technologies

Where needed the cell barcode can be detected in the index I1 or I2 file.

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