how to build bowtie2 index
bowtie2-build command is not clear
i have 1 genome reference starin want to compare with other 5 strain al data are fasta format
please who have time guide me step by step to learn this software
the first step I have the 6 genomes in my computer downloaded from NCBI AS fasta file want to do the genome index
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sh_shaddad77 •
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Bowtie is for short read data. If you have 5 very large fastas, you don't want this software.
this software used to compare whole-genome strain 13 Mb
Not exactly sure what this comment means but swbarnes2 is totally right.
bowtie2alignes short reads against a reference. Genome comparisons is not a usecase.could you please have a look at this article he used bowtie for the same organism but i will do for more strain https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879973/
if i am in the right way please support me to use this software
This article uses
bowtieto align reads to a reference genome. You downloaded entire genome, that is a hugh difference.that means I am in the wrong way, so bowtie for short sequences, the alternative option is to use BWA. is it suitable for whole-genome alignment of 5 strains with the reference genome (CDC317) to call SNPs
please advice me
No, bwa is also a read aligner, not a genome aligner.
What is the aim of your work? Just identifying SNPs between bacterial assemblies? And then what?
my ultimate objective is to call SNPs, the organism is yeast what is thought looking or SNPs need whole genome alignment is that right ?