Is it possible to estimate execution time for Bowtie2 ?

Question

[Esther Brasil]

I have a reference that is 1Gb in size, and two sets of reads with the same size. How to estimate the execution time of Bowtie2 given the features of my machine?

Answer 1

[Devon Ryan]

Honestly, your best bet is to just align a million reads or so (see the -u option) and extrapolate from that.

[kaston]

Does execution time scale linearly with number of reads?

[Devon Ryan]

Approximately, yes.

Answer 2

[Ray Lee]

1. use `bowtie2-build` to build index for the reference: bowtie2-build reference**.fa a_custom_name_as_index_name

2. use bowtie to align reads to the reference geneme: bowtie2 -p thread_num -x a_custom_name_as_index_name -1 left_reads.fq -2 right_reads.fq -S output_alignment_results.sam

tophat/HAIST -> bowtie2