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I am new to metcat and attempting to assemble amplicon based sequence reads for a virus genome. I am wondering on the set of optimal parameters for a 16000 long genome with 1500-2500 long amplicon seq…
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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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Hello!
I'm experiencing some issues with RAMPART and I'm wondering if there is a solution available. I would like to know if anyone has been able to resolve similar problems.
In our laboratory, …
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Hi,
First, thanks for making this available.
This is more of a question rather than issue. So the coordinates given in the output are in the + strand or the - strand? So is the amplicon sequence…
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Hello there
Thanks a lot already for the work on this package!
I am trying to cluster 34,937,058 sequences of about 1000bp (18S amplicons) contained in a single fasta file, I'm using the following…
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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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After merging the reads and checking for the V3LOOP amplicon, check for T-cell receptor alpha and beta (TCA and TCB) matches. Take all of those matches, and report the most common nucleotide sequences…
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**Describe the parameter code you need**
Metabarcoding datasets usually come with relative abundances in terms of sequence reads per ASV or OTU. This is a request for terms for:
- Total abundanc…
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nextera transposases cannot insert at the extreme ends of amplicons. To handle these libraries, it would be necessary to enable partial matches with expected start sequences.
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@nbokulich, @mikerobeson, @BenKaehler - how important do you all think the region-specific classifiers are? My impression is that they offer fairly small classification performance gains relative to t…