bowtie2
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BenLangmead
A fast and sensitive gapped read aligner
I honestly haven't found any evidence online for future implementations of `bowtie2` on GPU. Is this planned at all?
Hi, I am using bowtie2-2.4.4 and tried using bowtie2-build to create indexes of this fasta file https://drive.google.com/drive/folders/1WS7v1cs32Q7yDo2_cYtyXElorOk08hJ-?usp=sharing, but the wrapper attempts and fails to create small (.bt2) indexes. It works...
Hi, I used two mouse genomes (mm10 and GRCm39) and aligned my fastq files ( Links from Bowtie2 website: **https://genome-idx.s3.amazonaws.com/bt/mm10.zip** **and** https://genome-idx.s3.amazonaws.com/bt/GRCm39.zip** ). In comparision, the alignment work same is...
Hi, when testing the uBam alignment with the `--preserve-tags` flag, I noticed the the `@RG` header and the `RG` tag got left behind. Is this something that can be fixed?...
Hi. Complete newb here: I haven't compiled code since 1980s on IBM 3084 System/370 command line machines. Hope I'm not wasting your time. I saw the previous issue about asm,...
which was removed in https://github.com/BenLangmead/bowtie2/commit/acbc571bf7a637692e71c51e6700e02b23db1c4c
Hi, I have just started learning bowtie2. I encountered a problem with database indexing with bowtie2-build command: indexing runs through but the output doesn't have .rev files, thus preventing me...
I locally aligned 2x150 bp reads and found paired reads that have insert size 0; however, both reads are mapped and the insert sizes are under the --maxins value. Here...
I made several updates to the index sidebar and added a news item regarding levioSAM
Hi. I see this repository still uses travis-ci.org. Note Travis-ci.org shut down will occur on May 31, 2021. https://blog.travis-ci.com/2021-05-07-orgshutdown The `arch: arm64`, `arch: ppc64le`, `arch: s390x` free unlimited builds for...
