update documentation for 1.2.5-dev

<p><img src="https://img.shields.io/docker/automated/tomkellygenetics/universc?label=docker%20local%20build" alt="Docker Manual build" /> <img src="https://img.shields.io/docker/cloud/automated/tomkellygenetics/universc?label=docker%20cloud%20build" alt="Docker Cloud Build" /> <img src="https://img.shields.io/docker/cloud/build/tomkellygenetics/universc?label=cloud%20build" alt="Docker Cloud Status" /> <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><img src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.5" alt="Docker Image Version (tag latest semver)" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%22layers@1.2.4%22" alt="MicroBadger Layers (latest)" /> <img src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.4?label=%22image%20size@1.2.4" alt="Docker Image Size (v1.2.4)" /> <img src="https://img.shields.io/docker/v/tomkellygenetics/universc/latest" 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/latest" alt="Docker Image Size (latest)" /></p>

<p><img src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.5-dev" alt="Docker Image Version (tag latest semver)" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%22layers@1.2.5-dev%22" alt="MicroBadger Layers (latest)" /> <img src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.5-dev?label=%22image%20size@1.2.5-dev" alt="Docker Image Size (v1.2.5-dev)" /> <img src="https://img.shields.io/docker/v/tomkellygenetics/universc/latest" 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/latest" alt="Docker Image Size (latest)" /></p>

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cat Sample1_I2_file.fastq.gz Sample2_I2_file.fastq.gz Sample3_I2_file.fastq.gz &gt; Combined_I2_file.fastq.gz</code></pre>

<p>As this needs to done on a case-by-case basis it has not been implemented by the UniverSC core functions. We provide this workaround for using published data and data already processed by sequencing facilities. Please contact the maintainers or file an issue on GitHub if you are having problems with this case.</p>

<h4 id="custom-inputs">Custom inputs</h4>

<p>Custom inputs are also supported by giving the name &quot;custom&quot; and length of barcode and UMI separated by a &quot;_&quot; 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>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>

<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>

<h3 id="citation">Citation <span id="Citation"><span></h3>

<p>Please cite our publication when you use our software as follows:</p>

<p>Battenberg, K., Kelly, S.T., Ras, R.A., Hetherington, N.A., Hayashi, K., and Minoda, A. (2022) A flexible cross-platform single-cell data processing pipeline. <e>Nat Commun</e> <b>13</b>(1): 1-7. https://doi.org/10.1038/s41467-022-34681-z</p>

<p>Battenberg, K., Kelly, S.T., Ras, R.A., Hetherington, N.A., Hayashi, K., and Minoda, A. (2022) A flexible cross-platform single-cell data processing pipeline. <em>Nat Commun</em> <strong>13</strong>(1): 1-7. https://doi.org/10.1038/s41467-022-34681-z</p>

<pre><code>@Article{pmid36369450,

        author="Battenberg, K.  and Kelly, S. T.  and Ras, R. A.  and Hetherington, N. A.  and Hayashi, M.  and Minoda, A. ",

        title="{{A} flexible cross-platform single-cell data processing pipeline}",

        URL = {https://doi.org/10.1038/s41467-022-34681-z}

}</code></pre>

<p>The preprint can also be found here:</p>

<p>Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021) UniverSC: a flexible cross-platform single-cell data processing pipeline. bioRxiv 2021.01.19.427209; doi: <a href="https://doi.org/10.1101/2021.01.19.427209">https://doi.org/10.1101/2021.01.19.427209</a> package version 1.2.4. <a href="https://github.com/minoda-lab/universc">https://github.com/minoda-lab/universc</a></p>

<p>Kelly, S.T., Battenberg K., Hetherington, N.A., Hayashi, K., and Minoda, A. (2021) UniverSC: a flexible cross-platform single-cell data processing pipeline. bioRxiv 2021.01.19.427209; doi: <a href="https://doi.org/10.1101/2021.01.19.427209">https://doi.org/10.1101/2021.01.19.427209</a> package version 1.2.5-dev. <a href="https://github.com/minoda-lab/universc">https://github.com/minoda-lab/universc</a></p>

<pre><code>@article {Kelly2021.01.19.427209,

        author = {Kelly, S. Thomas and Battenberg, Kai and Hetherington, Nicola A. and Hayashi, Makoto and Minoda, Aki},

        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},

   index: 1

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

   index: 2

date: "Tuesday 18 October 2022"

date: "Wednesday 07 December 2022"

output:

  prettydoc::html_pretty:

       theme: cayman

The preprint can also be found here:

Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021)

Kelly, S.T., Battenberg K., Hetherington, N.A., Hayashi, K., and Minoda, A. (2021)

UniverSC: a flexible cross-platform single-cell data processing pipeline.

bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.1101/2021.01.19.427209](https://doi.org/10.1101/2021.01.19.427209)

package version 1.2.5-dev. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)