Very new to Bowtie2 but I'm trying to run it to align two bacterial genomes globally. Not sure which command to run, and the documentation makes it seem like this isn't possible.
I have both genomes as FASTA files. I run bowtie2-build -f $first_fasta on the first one and then I tried running bowtie2 -p 8 -x $db_name -f $second_fasta -S $result_file. My system has about 9 GB RAM available for the process but seems to quit because of low memory... I only need one alignment for this so I tried adding -k 1, but that didn't seem to help either (I've also done this with and without the -a param with the same results).
The error message is:
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
(ERR): bowtie2-align exited with value 3
Perhaps there is a totally different series of parameters I'm missing? Can Bowtie2 even do these kind of global alignments?
Thanks so much in advance!
EDIT 1: I'm working on a 64-bit Windows system so I cannot use mummer, minimap2, or mugsy (or any mummer-based program for that matter).
Are you doing synteny analysis?
I'm planning on looking at variable tandem repeats in the two strains (the global alignment is simply to help slim down the search space).
This doesn't sound like the appropriate tool for the job. Have a look at minimap2 or mummer, for example.
Interesting... I must admit I haven't heard of either of these, but since I'm building a Python wrapper for the whole thing, it appears both of these programs have Python equivalents (minimap2 and mummer). I'll look into both a bit more (I'm sure they go over this more in the documentation), but do either of these programs output an alignment as a BED file or something similar? [EDIT: I should've mentioned I'm running on a Windows system and it appears mummer is not Windows-compatible?] [EDIT 2: spent a while trying to get mugsy to work on Windows before realizing it is also built on mummer and is non-Windows-compatible]
Minimap2 provides alignments in PAF (pairwise Alignment Format), which might be what you are looking for...