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I'll use this issue to document steps to build a `k=31,scaled=1000` index for SRA metagenomes. This is the same process used for the current `k=21,scaled=1000` index in branchwater.sourmash.bio, but c…
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Hi Tobias
I haven't dug closely into the source code for this, so apologies if this question is a bit lazy:
What are the metrics affects by using the optional `--bed` flag for `alfred qc`?
I…
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Hi,
I wonder why you did not need to adjust the numbering of reported changes. I just want to add an arbitrary number to the nuc positions before the output is created.
To get around it, I padde…
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**Describe the bug**
SARS-CoV-2 variant BA.2.86 frequently has a 12 basepair insertion in Spike protein, which should be called as
MN908947.3 21608 . GTTAA GTCATGCCGCTGTTTAA
Ho…
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What does the option `--max-memory` do?
I am getting Killed signal because of out of memory but I already set this option so it seems it's not working.
`python /phasebook/scripts/phasebook.py -i…
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Thank you for developing the Cyanoseq database, which is very helpful for aquatic microbial research. I want to use Cyanoseq database on my 16S rRNA gene amplicon sequencing data. I downloaded CyanoSe…
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Hello, not sure if this is the right place to ask this question, but I will give it a try. As regards the publication i: https://doi.org/10.1101/213470, have you added the SynMock plasmids directly in…
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**Is your feature request related to a problem? Please describe.**
I think it's quite common that FLASH can't really merge the PE reads, For example:
- 1. amplicon sequence too long or too short…
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**How do I specify to trim partial sequences when supplying a fasta file of the sequences to be trimmed?**
I have amplicon sequencing data and I want to use cutadapt to remove FWD and REV amplicon …
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Hello all,
Just wanted to let people know what tools I'm working on (or might work on in the future), in case anyone else is interested in these.
I'm concentrating on RNA-seq/ChIP-seq/ATAC-seq wo…