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Marcel Martin (@marcelm@genomic.social) @marcelm_
Joined May 2014
  • Tweets 36
  • Following 71
  • Followers 141
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To celebrate 400 stars ⭐️on GitHub, Cutadapt 4.1 ✂️is now available. It can find rightmost adapter occurrences (closing a 5 year old issue) and allows you to use search parameters together with "file:a.fa" cutadapt.readthedocs.io/en/s…
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Marcel Martin (@marcelm@genomic.social) retweeted
Michael Ratz@ratz_michael
9 Mar 2022
Proud to present our cover art created by @Ella_Maru studio on the March issue of @NatureNeuro! We tried to illustrate how genetic barcodes can be used to reveal the relations between “simple” progenitor cells and “complex” differentiated cells in the brain. Take a look 👀
Nature Neuroscience
@NatureNeuro
8 Mar 2022
Our March issue is now live! nature.com/neuro/volumes/25/…
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Marcel Martin (@marcelm@genomic.social) retweeted
Michael Ratz@ratz_michael
24 Feb 2022
Great way to end the day: seeing our paper on clonal tracing in the mouse brain via single-cell and spatial transcriptomics in @NatureNeuro nature.com/articles/s41593-0… Many thanks to @leonie_vberlin Ludvig Larsson @marcelm_ Jakub Westholm @GioeleLaManno @joalunatkthse @FrisenJonas

Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics

Nature Neuroscience - Ratz et al. present an easy-to-use method to barcode progenitor cells, enabling profiling of cell phenotypes and clonal relations using single-cell and spatial...

nature.com
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I’ve published type annotations for pysam pypi.org/project/pysam-stubs… (for use with Mypy, PyCharm etc.) Hopefully to be integrated into pysam github.com/pysam-developers/…
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Cutadapt 3.5 released; it can write statistics in JSON format: cutadapt.readthedocs.io/en/s… Pro tip: Use jq to extract the info you need, such as the number of found adapters: jq '.adapters_read1[0].total_matches' file.cutadapt.json
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Marcel Martin (@marcelm@genomic.social) retweeted
Michael Ratz@ratz_michael
2 Sep 2021
Very excited to share our #preprint on TREX and Space-TREX in the mouse brain! Huge thanks to @leonie_vberlin, Ludvig Larsson, Marcel Martin, Jakub Westholm, @GioeleLaManno, @joalunatkthse and @FrisenJonas! Out now on @biorxiv_neursci 👉👉👉 biorxiv.org/content/10.1101/…

Cell types and clonal relations in the mouse brain revealed by single-cell and spatial transcript...

The mammalian brain contains a large number of specialized cells that develop from a thin sheet of neuroepithelial progenitor cells[1][1],[2][2]. Recently, high throughput single-cell technologies...

biorxiv.org
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Cutadapt 2.8 just released. It comes with a --revcomp option: This checks both the read and its reverse complement for an adapter and swaps it if necessary. Changelog at cutadapt.readthedocs.io/en/l…
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Cutadapt 2 is out! Focus was on speed and removing ancient features. But most importantly, I’ve added an animated progress bar ;-) cutadapt.readthedocs.io/en/s… [ 8<-------] [ 8=-------] [ 8<------]
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Our read-based phasing tool WhatsHap is now available in version 0.18 (pip/PyPI bioconda packages). New HapCHAT phasing algorithm integrated doi.org/10.1186/s12859-018-2… and bugfixes whatshap.readthedocs.io/en/l… @tobiasmarschal @m_d_patterson

HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads

BMC Bioinformatics - Haplotype assembly is the process of assigning the different alleles of the variants covered by mapped sequencing reads to the two haplotypes of the genome of a human...

link.springer.com
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Cutadapt 1.18 is now available with a couple of new features such as setting parameters individually per adapter. cutadapt.readthedocs.io/en/s…

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Now comes the fun part: I’ll finally remove colorspace support (happy you if you don’t know what that is) and switch to Python 3 only for the next release. #Python3
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Cutadapt 1.17 released with support for a new “non-internal” adapter type and a fix for running under Python 3.7. cutadapt.readthedocs.io/en/s…
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Marcel Martin (@marcelm@genomic.social) retweeted
Tobias Marschall@tobiasmarschal
9 Feb 2018
Excited to announce that we are hiring a Software Engineer dedicated to WhatsHap (whatshap.readthedocs.io/en/l…), see job ad (uni-saarland.de/fileadmin/us…). Funded by DFG's Research Software Sustainability program (dfg.de/en/research_funding/p…).
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Cutadapt 1.15 released with multi-core support! Use --cores=N and enjoy the speedup 😀. (See the docs for some limitations.) cutadapt.readthedocs.io/en/s…

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Cutadapt 1.14 fixes some smaller bugs and an installation issue affecting some Python 3 users cutadapt.readthedocs.io/en/s…
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Cutadapt 1.13 released with some bug fixes, better parameter sanity checking and more flexible linked adapters cutadapt.readthedocs.io/en/s…

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Cutadapt 1.12 adds documentation improvements and a (small) new feature: Trimming reads to a fixed length. cutadapt.readthedocs.io/en/s…
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Give it a try! WhatsHap: fast and accurate read-based phasing biorxiv.org/content/early/20…
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cutadapt 1.10 released with support for "linked adapters" (5'/3' adapter pairs) and NextSeq-specific trimming cutadapt.readthedocs.io/en/s…
Marcel Martin (@marcelm@genomic.social) retweeted
Johannes Köster (@johanneskoester.bsky.social)@johanneskoester
25 Apr 2016
Visit #bioconda at bioconda.github.io and choose from over 1000 bioinformatics tools via "conda install <toolname>"!

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