Marcel Martin (@[email protected])

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/stable/chan…

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 👀

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/s4159… Many thanks to @leonie_vberlin Ludvig Larsson @marcelm_ Jakub Westholm @GioeleLaManno @joalunatkthse @FrisenJonas

I’ve published type annotations for pysam pypi.org/project/pysam-… (for use with Mypy, PyCharm etc.) Hopefully to be integrated into pysam github.com/pysam-develope…

Cutadapt 3.5 released; it can write statistics in JSON format: #json-report-format" target="_blank" rel="nofollow noopener">cutadapt.readthedocs.io/en/stable/refe… 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

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/10.110…

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/latest/chan…

@StevenNHart Cutadapt’s demultiplexing is based on adapter trimming: The best matching adapter determines which output the read is sent to. At the moment, you cannot have adapters that don’t affect demultiplexing, so it’s best to run it twice.

Cutadapt 2 is out! Focus was on speed and removing ancient features. But most importantly, I’ve added an animated progress bar ;-) #v2-0-2019-03-06" target="_blank" rel="nofollow noopener">cutadapt.readthedocs.io/en/stable/chan… [ 8<-------] [ 8=-------] [ 8<------]

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… and bugfixes whatshap.readthedocs.io/en/latest/chan… @tobiasmarschal @m_d_patterson

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

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

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/stable/chan…

@David_McGaughey @jdidion @biorxivpreprint @BioMickWatson It is since 1.15 (released in November)

Excited to announce that we are hiring a Software Engineer dedicated to WhatsHap (whatshap.readthedocs.io/en/latest/inde…), see job ad (uni-saarland.de/fileadmin/user…). Funded by DFG's Research Software Sustainability program (dfg.de/en/research_fu…).

@thatdnaguy A reader process splits data into 4 MB chunks and sends them to worker processes, which parse the FASTQ and trim reads. Main process collects, orders and writes results. No temp files.

Cutadapt 1.15 released with multi-core support! Use --cores=N and enjoy the speedup 😀. (See the docs for some limitations.) #v1-15-2017-11-23" target="_blank" rel="nofollow noopener">cutadapt.readthedocs.io/en/stable/chan…

@TommyCarstensen It works on streams, both for input and output, just use "-" as file name (for input, it even autodetects FASTA vs FASTQ)

Cutadapt 1.14 fixes some smaller bugs and an installation issue affecting some Python 3 users cutadapt.readthedocs.io/en/stable/chan…

Cutadapt 1.13 released with some bug fixes, better parameter sanity checking and more flexible linked adapters #v1-13-2017-03-16" target="_blank" rel="nofollow noopener">cutadapt.readthedocs.io/en/stable/chan…