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Hi Mikko,
Does GraphAligner only permit alignments that use **L** (link) lines to connect segments? or will it also report paths where a read aligns across two contigs that are not connected in t…
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Currently, judging by the Readme, the only Linux version offered is snap, which is kinda *buntu/Canonical-centric and maybe should not be the only format available, at least in my opinion, having more…
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- Whatshap - 1.7, Python - 3.10.8
- Conda
- Which command-line parameters you used
- whatshap haplotag -o haplotaggedchr22.bam --reference Homo_sapiens_assembly38.fasta --region chr22 phased.vcf.…
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Hi,
In your paper, you say that you "discard those reads with low alignment quality, including MAPQ < 20, aligned length < 30 nt and FLAG with UNMAP, SECONDARY, QCFAIL (and DUP if UMI is not applic…
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Primary interest: HiFi reads
Requested output by Pille:
`read depth, both with and without secondary alignments`
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Hi,
I successfully run orthofinder using the protein sequences, but I get an error when I run it again using the nucleotide sequences from the same species.
I have DNA sequences for 71 species. Th…
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Hi, thanks for the amazing tool by the way! I'm having an issue where RAxML can't parse alignments for which there are sequences made entirely of undetermined characters:
[e] error while refining…
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Hello,
I am running Clinker on a server (installed via conda) for five genomes (from the same genus); gbk files were downloaded from GenBank. I use the following command:
`clinker ./genomes/*.gbk…
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### Because
The generosity of allowing short form for annotation `id` values provides almost no benefit (besides saving some bytes) while adding lots of technical debt and bugs. For example, we hav…
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Hi,
I'm using MMseqs2 for all-vs-all alignments. As indicated in the user guide pdf, I'm using the bash script to perform a fake prefiltering step before aligning. That seems to work, as all alignm…