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Hi,
My sequencing data is amplicon sequencing that some regions got excessive coverage. I wonder if I can set a maxi coverage in Pisces.
Thank you!
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I am trying to run velveth on my paired files but facing the following error:
[0.000000] Velvet can't handle k-mers as long as 33! We'll stick to 31 if you don't mind.
[0.024794] Reading FastA fil…
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If I manually split a 300kb seed into two 100kb seeds, what is the difference in the AA running results?
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We want to start to accumulate a bibliography of papers that describe oligotypes and amplicon and exact sequence variants. Add new references to this thread.
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```
hp_pairwise_align --amplicons_fa haphpipe_assemble_02/final.fna --ref_fa ../HIV_B.K03455.HXB2.fasta --ref_gtf ../HIV_B.K03455.HXB2.gtf --outdir haphpipe_assemble_02
[--- pairwise_align ---] U…
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In next release of the the typing tool support for single and multi FASTA files is desirable allowing to for assembled gp60 or 18S amplicon(s) to be typed assuming one amplicon sequence per sample and…
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See https://github.com/Zymo-Research/figaro
This would be primarily for amplicons with a minor overlap; might work best as a simple helper script.
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Hi everyone,
I was analysing amplicon reads from 16s V3-V4, using 341F-806R primer set. The quality of the reads are fairly good:
. I have successfully built the SILVA database. However, I wanted to know about processing multiple samples. Can …
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I initially discovered this while building the 2024.5 docs, but also replicated locally. Within a 2024.5 amplicon environment (on mac OS) the command in PD mice that utilizes ancombc with `donor * gen…