Commit bb84c1a2 authored by TomKellyGenetics's avatar TomKellyGenetics
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update branches in README

parent cd9bbed9

README.Rmd

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![Docker Image Size (latest)](https://img.shields.io/docker/image-size/tomkellygenetics/universc?sort=date)



![Docker CI](https://github.com/minoda-lab/universc/workflows/CI%20to%20Docker%20hub/badge.svg)

![Docker compose](https://github.com/minoda-lab/universc/workflows/Docker%20Compose%20Actions/badge.svg)

![Docker compose](https://github.com/minoda-lab/universc/workflows/Docker%20compose%20build/badge.svg)



![Actions Build](https://github.com/minoda-lab/universc/workflows/Docker%20Test/badge.svg)

![Actions Tests](https://github.com/minoda-lab/universc/workflows/Run%20tests%20in%20Docker/badge.svg)

![Actions Call](https://github.com/minoda-lab/universc/workflows/Docker%20Test%20Calling%20Dependencies/badge.svg)

![Actions Build](https://github.com/minoda-lab/universc/workflows/Docker%20container%20test/badge.svg)

![Actions Tests](https://github.com/minoda-lab/universc/workflows/Run%20all%20tests%20in%20Docker/badge.svg)

![Actions Call](https://github.com/minoda-lab/universc/workflows/Docker%20build%20image/badge.svg)



![Test 10x Genomics](https://github.com/minoda-lab/universc/workflows/Test%2010x%20Genomics/badge.svg)

![Test DropSeq](https://github.com/minoda-lab/universc/workflows/Test%20DropSeq%20%2F%20Nadia/badge.svg)

![Test ICELL8](https://github.com/minoda-lab/universc/workflows/Test%20ICELL8/badge.svg)



![Test SCI-Seq](https://github.com/minoda-lab/universc/workflows/Test%20SCI%2DSeq/badge.svg)

![Test inDrops v3](https://github.com/minoda-lab/universc/workflows/Test%20inDrops%20v3/badge.svg)

![Test Smart-Seq3](https://github.com/minoda-lab/universc/workflows/Test%20Smart%2DSeq3/badge.svg)



# UniverSC



**Single-cell processing across technologies**

README.html

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<p><img src="https://img.shields.io/docker/stars/tomkellygenetics/universc" alt="Docker Stars" /> <img src="https://img.shields.io/docker/pulls/tomkellygenetics/universc" alt="Docker Pulls" /></p>

<p><embed src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.0.2" /> <embed src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/1.0.2" /> <embed src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.0.2" /></p>

<p><img src="https://img.shields.io/docker/v/tomkellygenetics/universc" alt="Docker Image Version (latest by date)" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest" alt="MicroBadger Layers (latest)" /> <img src="https://img.shields.io/docker/image-size/tomkellygenetics/universc?sort=date" alt="Docker Image Size (latest)" /></p>

<p><img src="https://github.com/minoda-lab/universc/workflows/CI%20to%20Docker%20hub/badge.svg" alt="Docker CI" /> <img src="https://github.com/minoda-lab/universc/workflows/Docker%20Compose%20Actions/badge.svg" alt="Docker compose" /></p>

<p><img src="https://github.com/minoda-lab/universc/workflows/Docker%20Test/badge.svg" alt="Actions Build" /> <img src="https://github.com/minoda-lab/universc/workflows/Run%20tests%20in%20Docker/badge.svg" alt="Actions Tests" /> <img src="https://github.com/minoda-lab/universc/workflows/Docker%20Test%20Calling%20Dependencies/badge.svg" alt="Actions Call" /></p>

<p><img src="https://github.com/minoda-lab/universc/workflows/CI%20to%20Docker%20hub/badge.svg" alt="Docker CI" /> <img src="https://github.com/minoda-lab/universc/workflows/Docker%20compose%20build/badge.svg" alt="Docker compose" /></p>

<p><img src="https://github.com/minoda-lab/universc/workflows/Docker%20container%20test/badge.svg" alt="Actions Build" /> <img src="https://github.com/minoda-lab/universc/workflows/Run%20all%20tests%20in%20Docker/badge.svg" alt="Actions Tests" /> <img src="https://github.com/minoda-lab/universc/workflows/Docker%20build%20image/badge.svg" alt="Actions Call" /></p>

<p><img src="https://github.com/minoda-lab/universc/workflows/Test%2010x%20Genomics/badge.svg" alt="Test 10x Genomics" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20DropSeq%20%2F%20Nadia/badge.svg" alt="Test DropSeq" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20ICELL8/badge.svg" alt="Test ICELL8" /></p>

<p><img src="https://github.com/minoda-lab/universc/workflows/Test%20SCI%2DSeq/badge.svg" alt="Test SCI-Seq" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20inDrops%20v3/badge.svg" alt="Test inDrops v3" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20Smart%2DSeq3/badge.svg" alt="Test Smart-Seq3" /></p>

<h1 id="universc">UniverSC</h1>

<p><strong>Single-cell processing across technologies</strong></p>

<hr />
@@ -65,7 +66,7 @@ 
</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>We are developing technologies to support dual indexes and full length scRNA kits.</p>

<p>Experimental technologies (not yet supported): - inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 - Sci-Seq (8bp UMI, 10bp barcode): sciseq - SPLiT-Seq (10bp UMI, 18bp barcode): splitseq - SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad</p>

<p>Experimental technologies (not yet supported): - inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 - Sci-Seq (8bp UMI, 22bp barcode): sciseq - SPLiT-Seq (10bp UMI, 18bp barcode): splitseq - SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad</p>

<h4 id="dual-indexing">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;\
@@ -484,7 +485,7 @@ Mandatory arguments to long options are mandatory for short options too. 


                                Experimental technologies (not yet supported):

                                  inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

                                  Sci-Seq (8bp UMI, 10bp barcode): sciseq

                                  Sci-Seq (8bp UMI, 22bp barcode): sciseq



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

README.md

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   index: 1

 - name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan"

   index: 2

date: "Wednesday 27 January 2021"

date: "Sunday 31 January 2021"

output:

  prettydoc::html_pretty:

       theme: cayman
@@ -45,16 +45,20 @@ tags: 
![Docker Image Size (latest)](https://img.shields.io/docker/image-size/tomkellygenetics/universc?sort=date)



![Docker CI](https://github.com/minoda-lab/universc/workflows/CI%20to%20Docker%20hub/badge.svg)

![Docker compose](https://github.com/minoda-lab/universc/workflows/Docker%20Compose%20Actions/badge.svg)

![Docker compose](https://github.com/minoda-lab/universc/workflows/Docker%20compose%20build/badge.svg)



![Actions Build](https://github.com/minoda-lab/universc/workflows/Docker%20Test/badge.svg)

![Actions Tests](https://github.com/minoda-lab/universc/workflows/Run%20tests%20in%20Docker/badge.svg)

![Actions Call](https://github.com/minoda-lab/universc/workflows/Docker%20Test%20Calling%20Dependencies/badge.svg)

![Actions Build](https://github.com/minoda-lab/universc/workflows/Docker%20container%20test/badge.svg)

![Actions Tests](https://github.com/minoda-lab/universc/workflows/Run%20all%20tests%20in%20Docker/badge.svg)

![Actions Call](https://github.com/minoda-lab/universc/workflows/Docker%20build%20image/badge.svg)



![Test 10x Genomics](https://github.com/minoda-lab/universc/workflows/Test%2010x%20Genomics/badge.svg)

![Test DropSeq](https://github.com/minoda-lab/universc/workflows/Test%20DropSeq%20%2F%20Nadia/badge.svg)

![Test ICELL8](https://github.com/minoda-lab/universc/workflows/Test%20ICELL8/badge.svg)



![Test SCI-Seq](https://github.com/minoda-lab/universc/workflows/Test%20SCI%2DSeq/badge.svg)

![Test inDrops v3](https://github.com/minoda-lab/universc/workflows/Test%20inDrops%20v3/badge.svg)

![Test Smart-Seq3](https://github.com/minoda-lab/universc/workflows/Test%20Smart%2DSeq3/badge.svg)



# UniverSC



**Single-cell processing across technologies**
@@ -166,7 +170,7 @@ We are developing technologies to support dual indexes and full length scRNA kit 


Experimental technologies (not yet supported):

-  inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

-  Sci-Seq (8bp UMI, 10bp barcode): sciseq

-  Sci-Seq (8bp UMI, 22bp barcode): sciseq

-  SPLiT-Seq (10bp UMI, 18bp barcode): splitseq

-  SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
@@ -988,7 +992,7 @@ Mandatory arguments to long options are mandatory for short options too. 


                                Experimental technologies (not yet supported):

                                  inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

                                  Sci-Seq (8bp UMI, 10bp barcode): sciseq

                                  Sci-Seq (8bp UMI, 22bp barcode): sciseq



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

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