User: BioinformaticsLad

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Posts by BioinformaticsLad

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Comment: C: Tool to calculate insertion, deletion, mismatch rate in alignments?
... [Alfred][1] turned out to be exactly what I was looking for. [1]: https://github.com/tobiasrausch/alfred ...
written 3 days ago by BioinformaticsLad140
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Comment: C: Detection of antibiotic resistance genes in shotgun metagenomic samples
... I looked in Ariba more and the authors say it's not suitable for metagenomic samples ...
written 11 days ago by BioinformaticsLad140
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BBMap reformat.sh qahist statistics interpretation?
... I ran reformat.sh on a SAM file and the log seemed fine: Input is being processed as unpaired Input: 35583 reads 52857642 bases Output: 35583 reads (100.00%) 52857642 bases (100.00%) But then in the results, the sum of the all matched bases ...
bbmap written 4 weeks ago by BioinformaticsLad140
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Tool to calculate insertion, deletion, mismatch rate in alignments?
... I know samtools stats can quantify the mismatch rate in SAM files. But are there any tools that can also calculate insertions and deletions? ...
alignment written 4 weeks ago by BioinformaticsLad140 • updated 4 weeks ago by h.mon28k
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Comment: C: Filter human parasites from taxonomic profiling with Kraken
... Could you explain why? Do parasites tend to have higher mutation rates? ...
written 7 weeks ago by BioinformaticsLad140
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Comment: C: Detection of antibiotic resistance genes in shotgun metagenomic samples
... I thought about that, but it would take an inordinate amount of time. Each of my samples is 30Gbp! ...
written 7 weeks ago by BioinformaticsLad140
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Comment: C: Detection of antibiotic resistance genes in shotgun metagenomic samples
... I know baout Ariba but the analysis requires assembly. fARGene I don't know about - I'll check it out, thanks! ...
written 7 weeks ago by BioinformaticsLad140
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Detection of antibiotic resistance genes in shotgun metagenomic samples
... There are several pipelines for detection of ARGs using assembled contigs but I was wondering if anyone has had any luck performing ARG detection using raw reads? There's GROOT, which is quite new, so I'm not sure performance. ...
metagenomics written 7 weeks ago by BioinformaticsLad140 • updated 7 weeks ago by gb1.2k
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Comment: C: Shotgun metagenomics high duplication read rate - how high is too high?
... You bring up a good point about diversity and sequencing depth. I sequenced 30Gbps for each of my gut samples. Gut samples are typically not very high diversity (100-200 species). So could it be that we're simply sequencing too deeply? I'm thinking I should subsample my fastq down to 10Gbps before d ...
written 8 weeks ago by BioinformaticsLad140
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Comment: C: Shotgun metagenomics high duplication read rate - how high is too high?
... Hi, high read depth won't be a problem for me. I'm referring to sequence duplication - distinct reads that have more than one copy. For [example][1] [1]: http://hmp.ucalgary.ca/HMP/metagenomes/data/Iso3T/illumina/Iso3T.R1_fastqc/fastqc_report.html#M8 ...
written 8 weeks ago by BioinformaticsLad140

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Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Guppy basecaller ONT
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