bowtie2 --passthrough, what does it do???

Question

[mcrepeau]

I frequently see people use the --passthrough argument in their bowtie2 command lines, but I can't find any mention of that argument in the bowtie2 documentation. What does the argument do?

[mcrepeau]

Wow! That's pretty weird. Thanks for doing the experiment!

[GenoMax]

It is noted in bowtie2 code here: https://github.com/BenLangmead/bowtie2/blob/master/bowtie2

Answer 1

[ATpoint]

With a minimal example just tested the option. It seems it appends a line after every read in the SAM file (a concatenated version of the fastq entry) starting with @. This is critical as @ indicates a header line and when you pipe this output into samtools it will throw an error. The option is not even documented in the bowtie2 manual, I personally have never seen it. Not sure whether it might have been added for some development/debug purposes of the developers. Simply don't use it, it is not necessary and will break downstream tools.

$ cat foo.fq
@read1
TAGCTGAC
+
TAGCTGAC
@read2
AAA
+
CGA

$ bowtie2 -x foo --passthrough -U foo.fq
2 reads; of these:
  2 (100.00%) were unpaired; of these:
    2 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
@HD VN:1.0  SO:unsorted
@SQ SN:chr1 LN:30
@PG ID:bowtie2  PN:bowtie2  VN:2.4.2    CL:"/home/a/a_toen03/miniconda3/bin/bowtie2-align-s --wrapper basic-0 -x foo --passthrough -U foo.fq"
read1   4   *   0   0   *   *   0   0   TAGCTGAC    TAGCTGAC    YT:Z:UU
@read1%0ATAGCTGAC%0A+%0ATAGCTGAC%0A
read2   4   *   0   0   *   *   0   0   AAA CGA YT:Z:UU
@read2%0AAAA%0A+%0ACGA%0A