For reproducibility, Bowtie2 --reorder should be used
marcelm opened this issue · 1 comments
marcelm commented
When Bowtie2 runs multithreaded, the output order of the mapped reads is not the same as in the input FASTQ file. Even after sorting, the output BAM file is not the same when running the same pipeline twice, which is bad for reproducibility.
To solve this, we can simply add --reorder to the Bowtie2 command-line options. I will test how this changes runtime and open a PR.