Marcel Martin (@[email protected])

36 posts

Marcel Martin (@marcelm@genomic.social)

Marcel Martin (@[email protected])

@marcelm_

Katılım Mayıs 2014
71 Takip Edilen140 Takipçiler
Marcel Martin (@marcelm@genomic.social)
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
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Marcel Martin (@marcelm@genomic.social)
@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.
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Marcel Martin (@marcelm@genomic.social)
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<------]
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Marcel Martin (@marcelm@genomic.social)
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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Marcel Martin (@marcelm@genomic.social)
@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.
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Marcel Martin (@marcelm@genomic.social)
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…
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Marcel Martin (@marcelm@genomic.social)
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…
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