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Hi,
Thanks for a great tool. I am playing around with genotyping amplicon data from Nanopore sequencing. I can get Straglr to call certain STRs but not others, and I wonder if I need to do somethin…
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### Ask away!
I am running the wf-amplicon on PCR amplicons covering a complete virus genome (4 overlapping long amplicons per sample, pooled in one barcode) and map the reads to a reference genome o…
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Hi,
I have analysed ITS1 amplicons from fungal samples (leaf endophytes) using kraken2 and the PlusPFP-16 indices provided by Ben Langmead.
These amplicons were trimmed for PCR primer sequences, b…
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current fix has a more stringent filtering of non overlapping reads in dada2. Some of those reads can be stitched back and I think we can do a better job at merging those, but will require some thinki…
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Vsearch supports --fastq_join in which "sequences are not merged as with the fastq_mergepairs command, but simply joined with a gap."
**Addition Description**
It would work like the existing [me…
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Hi,
I'm using an amplicon kit which has tiled amplicons. These can create super amplicons, where the forward primer for amplicon 1 can form an 'super' amplicon with the reverse primer of amplicon2.
…
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Hi,
Great tool for implementing L. pneumophila SBT! Thanks.
I'm trying to call SBT using nanopore sequenced multiplex PCR amplicons. However, I get "no product" results for some of the alleles. S…
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Out of curiousity, the description says:
> Flash2 has some improvements from flash_1 including new logic from innie and outie overlaps as well as some initial steps for flash for amplicons
I saw …
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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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Hello! Thanks for putting together CliqueSNV - the ability to leverage long reads should be really powerful across different fields I think. I was curious if it would be possible to use long reads tha…