Minimum read length aligned by bowtie

Microbial community profiling MetaPhlAn
1

We know in metaphlan, bowtie2 discards reads shorter than 70 bp by default. Suppose in a file each read has two spots and each spot length is 44bp. In that case, will the reads be discarded?

Thanks,
DC7

2

Since 44bp is less than 70bp, both spots will be discarded.

1 Like