bowtie2
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BenLangmead
A fast and sensitive gapped read aligner
Hello. I would like to ask a question about making a bowtie2 database. I am using the kneaddata human genome + human contaminants file to decontaminate my data, which uses...
Hello, Thanks for writing great software and your work maintaining it. I ran into a vexing issue that would be easy to fix for people in the future. Somehow my...
Hi, I'm playing a little with bowtie2 scoring (for more flexibility) and I've noticed that if I multiply all scoring parameters by a factor of 10, I get slightly different...
The web page offers pre-built indexes, such as H. sapiens, GRCh38 no-alt but not a version with alternate contigs. May there be a paragraph added to the MANUAL file discussing...
Hi, I noticed a part of the fastq header is interpreted as a fastq comment on alignment. version: `2.4.5` command: `bowtie2 --local --fast-local -p 10 -x /Shared/references/Hsapiens/hg38-noalt/bowtie2/hg38-noalt.fa --sam-append-comment -1 fq_1.fastq...
According to the manual: ``` As of Bowtie2 v2.4.0, individual preset values can be overridden by providing the specific options e.g. the configured seed length of 20 in the [--very-senitive]...
`renameIdxFiles` in `bt2_build.cpp` does not respect `--quiet` Perhaps a `if (verbose)` around the body? ~~~ /opt/bowtie2/bowtie2-build-s version 2.4.5 64-bit Built on 51df6955ec49 Mon Jan 17 00:22:22 UTC 2022 Compiler: gcc...
Where does `bowtie2-inspect` write the FASTA? I have the GRCh38_noalt_as folder full of .bt2 files but I would like the FASTA from whence they came in order to use bedtools'...
Hi, Using Bowtie2 `2.4.4` or `bug-fixes` I found that certain output bams break certain downstream tools like fgbio `ClipBam` and Picard `ValidateSamFile`. I traced the problem back to how Bowtie2...
Bowtie2 (2.4.4) outputs the `@HD` line in the header as follows: `@HD VN:1.0 SO:unsorted` Many downstream tools e.g. `fgbio` require query-grouped / name-collated reads but rely on the `@HD` header...