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…

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… Tobias Marschall Murray Patterson

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/stable/chan… [ 8<-------] [ 8=-------] [ 8<------]

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…

Very excited to share our #preprint on TREX and Space-TREX in the mouse brain! Huge thanks to Leonie, Ludvig Larsson, Marcel Martin, Jakub Westholm, Gioele La Manno, Joakim Lundeberg and Jonas Frisén! Out now on bioRxiv Neuroscience 👉👉👉 biorxiv.org/content/10.110…

Cutadapt 3.5 released; it can write statistics in JSON format: 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

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…

Great way to end the day: seeing our paper on clonal tracing in the mouse brain via single-cell and spatial transcriptomics in Nature Neuroscience nature.com/articles/s4159… Many thanks to Leonie Ludvig Larsson Marcel Martin (@[email protected]) Jakub Westholm Gioele La Manno Joakim Lundeberg Jonas Frisén

Proud to present our cover art created by Ella Marushchenko studio on the March issue of Nature Neuroscience! 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 👀

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…

Visit #bioconda at bioconda.github.io and choose from over 1000 bioinformatics tools via "conda install <toolname>"!

cutadapt 1.10 released with support for "linked adapters" (5'/3' adapter pairs) and NextSeq-specific trimming cutadapt.readthedocs.io/en/stable/chan…

Give it a try! WhatsHap: fast and accurate read-based phasing biorxiv.org/content/early/…

Cutadapt 1.12 adds documentation improvements and a (small) new feature: Trimming reads to a fixed length. cutadapt.readthedocs.io/en/stable/chan…

Cutadapt 1.13 released with some bug fixes, better parameter sanity checking and more flexible linked adapters cutadapt.readthedocs.io/en/stable/chan…

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

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/stable/chan…

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…).