Marcel Martin (@[email protected])

[Marcel Martin (@[email protected]) @marcelm_]

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" https://t.co/UXop6GztN0

[Michael Ratz @ratz_michael]

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 👀

[Michael Ratz @ratz_michael]

Great way to end the day: seeing our paper on clonal tracing in the mouse brain via single-cell and spatial transcriptomics in @NatureNeuro

https://t.co/IwO5U1rAS9

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

[Marcel Martin (@[email protected]) @marcelm_]

I’ve published type annotations for pysam https://t.co/xyoxJUw6hd (for use with Mypy, PyCharm etc.) Hopefully to be integrated into pysam https://t.co/AQx662EX6H

[Marcel Martin (@[email protected]) @marcelm_]

Cutadapt 3.5 released; it can write statistics in JSON format:
https://t.co/7koNoXswJR

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

[Michael Ratz @ratz_michael]

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
👉👉👉
https://t.co/FawTGmEO1t

[Marcel Martin (@[email protected]) @marcelm_]

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 https://t.co/f2HcH5Fu7J

[Marcel Martin (@[email protected]) @marcelm_]

@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.

[Marcel Martin (@[email protected]) @marcelm_]

Cutadapt 2 is out! Focus was on speed and removing ancient features. But most importantly, I’ve added an animated progress bar ;-)
https://t.co/1Cfx4EWhS9
[ 8<-------]
[ 8=-------]
[ 8<------]

[Marcel Martin (@[email protected]) @marcelm_]

Our read-based phasing tool WhatsHap is now available in version 0.18 (pip/PyPI+bioconda packages). New HapCHAT phasing algorithm integrated https://t.co/NT1PhdAqHo and bugfixes https://t.co/20Ti6pgtpg @tobiasmarschal @m_d_patterson

[Marcel Martin (@[email protected]) @marcelm_]

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

[Marcel Martin (@[email protected]) @marcelm_]

Cutadapt 1.18 is now available with a couple of new features such as setting parameters individually per adapter. https://t.co/UXop6GztN0

[Marcel Martin (@[email protected]) @marcelm_]

Cutadapt 1.17 released with support for a new “non-internal” adapter type and a fix for running under Python 3.7. https://t.co/UXop6GztN0

[Marcel Martin (@[email protected]) @marcelm_]

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

[Tobias Marschall @tobiasmarschal]

Excited to announce that we are hiring a Software Engineer dedicated to WhatsHap (https://t.co/6cfyxtEcHV), see job ad (https://t.co/ILG2tb4aei). Funded by DFG's Research Software Sustainability program (https://t.co/xEOiX6hlkt).

[Marcel Martin (@[email protected]) @marcelm_]

@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.

[Marcel Martin (@[email protected]) @marcelm_]

Cutadapt 1.15 released with multi-core support! Use --cores=N and enjoy the speedup 😀. (See the docs for some limitations.) https://t.co/thM9me8liG

[Marcel Martin (@[email protected]) @marcelm_]

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

[Marcel Martin (@[email protected]) @marcelm_]

Cutadapt 1.14 fixes some smaller bugs and an installation issue affecting some Python 3 users https://t.co/UXop6GhSoq

[Marcel Martin (@[email protected]) @marcelm_]

Cutadapt 1.13 released with some bug fixes, better parameter sanity checking and more flexible linked adapters https://t.co/VFmryf3MMf