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I was running the latest version of Picard (v2.23.3) on some Influenza samples and ran into an issue because the sequence names contained parentheses which are no longer allowed in the SAM specificati…
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Dear author,
I found some more files than before based on 'human + HBV' genomes, they are **Chimeric.out.junction.circRNA** and **Chimeric.out.junction.circRNAmapped**.
What are they and whe…
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The step5 of OPERA-MS is "computation of Mash genomic distance against a database of 2,800 complete genomes".
```
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt
awk…
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I am trying to use ".importation_status.txt" output from CFML to see what genes are affected by recombination. From the issues in this github, I found out that CFML concatenates multiple loci sequence…
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Hi
The fastv is so convenient and nice to use for the provided test data. But I'm curious about how to make our own kmer file if we use customized virus fasta.
Thanks in adcvance for your reply
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Hello!
I am trying to use Arriba on a bit of an obscure genome (the woodchuck genome) to detect virus integration from a hybrid genome generated by `cellranger mkref`. I installed Arriba via Biocon…
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There are 957 Cov species in the NCBI taxonomy tree.
There are 4,236 complete genomes of Coronaviridae species in Genbank, which is ~4 complete genomes per species. List here:
[complete_cov_geno…
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For best taxonomy assignment and tree-building, we would ideally identify these "domains" per #195:
pp1ab: ADRP, nsp5 (3CLpro), nsp12 (RdRp), nsp13 (Hel), nsp14 (ExoN), nsp15 (NendoU) and nsp16 (O-…
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Hi,
I am trying to make a custom Kraken2 database with bacteria, archaea, fungi, viruses and some "added" genomes. It seems to work until I do the classification where I got only 25% of my reads c…
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Master tsv file for fist 1k assembler targets here:
[https://serratus-public.s3.amazonaws.com/rce/assembly/assembly_targets_first_1k.tsv](https://serratus-public.s3.amazonaws.com/rce/assembly/assem…