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Hi,
I love that you have made this tool. installed using conda and I ran this command "TideHunter -u barcode18_test.fastq > units3.fa" and get a file full of the split out subreads/repeats. Howev…
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I ran similar commands with the same data, only changing the -H setting.
`bcf consensus -H 1 -f reference.fa subject.vcf.gz > consensus_H1.fasta`
`bcf consensus -H 2 -f reference.fa subject.vcf.gz…
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Hi,
I'm having difficulty clustering using profiles when following the instructions in the wiki. Specifically I'm referring to this section:
```
# extract consensus sequences from profiles
…
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Hello,
I'll be soon getting data RNA-seq data with UMIs, and I was interested in running pair consensus decoding on the data. I noticed the paper's and bonito's implementation takes the reverse com…
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A user has asked for this option:
When using "-cluster_fast" VSEARCH builds consensus sequences considering terminal gaps in the alignment, so a lot of relevant sequence information on the flanking r…
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After running bwa index on my ref_geneA.fa file and running bwa mem on the ref and different species exome data, I then used samtools to sort and index the output files. I am now trying to get just th…
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Hi there,
I have two questions:
1. You have mentioned that "ONTbarcoder has been optimized for protein coding gene like COI. While **there are ways** to obtain consensus for length variable non …
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Hello,
I was wondering abou what reference HIV-1 version does sierra uses. According to the releases notes presented in https://hivdb.stanford.edu/page/release-notes/, the platform uses the Consens…
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Hi,
I have been using NGSpeciesID on a microbiome dataset with 90 samples (one fastq file per sample).
I use a for loop to loop through these samples with the following command:
```
for file in…
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Following the discussion in PR https://github.com/bulwark-security/bulwark-community-ruleset/pull/1, there's a consensus on improving the function to gracefully handle invalid UTF-8 sequences. The '�…