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BenLangmead / bowtie

An ultrafast memory-efficient short read aligner
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Axolotl genome index building with Bowtie 1.2.3 #96

Closed Gil-marquez closed 2 years ago

Gil-marquez commented 4 years ago

I'm trying to bowtie-build the axolotl genome with Bowtie 1.2.3, but the run never finishes even when using the --large-index option. I'm using Bowtie instead of bowtie 2 (which succesfully creates the index) because I have small reads (<=50 bp SE). The axolotl genome is about 32 Gb, is there any other way I can make a single index of this genome with Bowtie 1 and avoid creating multiple indexes after fractioning the sequence?

Has any one succesfully completed the bowtie-build for this genome?

Thanks in advance!

Thanks

Riptides commented 4 years ago

While I haven't tested personally, the changelog states that Bowtie v1.2.3 can now use Bowtie2 indexes, which should solve your problem.

ch4rr0 commented 2 years ago

I know this issue is over 2 years old now, but I believe that the fix for #124 should also resolve this one.

ch4rr0 commented 2 years ago

The change which seeks to address this issue has been released as part of v1.3.1. Feel free to reopen this tracker if the issue persists.