Bowtie 2 / HiSAT2

The module parses results generated by Bowtie 2 and HISAT2, ultrafast and memory-efficient tools for aligning sequencing reads to long reference sequences. Unfortunately, both tools have identical log output by default, so it is impossible to distinguish which tool was used.

Please note that the Bowtie 2 and HISAT2 logs are difficult to parse as they don’t contain much extra information (such as what the input data was). A typical log looks like this:

314537 reads; of these:
  314537 (100.00%) were paired; of these:
    111016 (35.30%) aligned concordantly 0 times
    193300 (61.46%) aligned concordantly exactly 1 time
    10221 (3.25%) aligned concordantly >1 times
    ----
    111016 pairs aligned concordantly 0 times; of these:
      11377 (10.25%) aligned discordantly 1 time
    ----
    99639 pairs aligned 0 times concordantly or discordantly; of these:
      199278 mates make up the pairs; of these:
        112779 (56.59%) aligned 0 times
        85802 (43.06%) aligned exactly 1 time
        697 (0.35%) aligned >1 times
82.07% overall alignment rate

The logs are from STDERR - some pipelines (such as Cluster Flow) print the command before this, so MultiQC looks to see if this can be recognised in the same file. If not, it takes the filename as the sample name.

Bowtie 2 and HISAT2 are used by other tools too, so if your log file contains the word bisulfite, MultiQC will assume that this is actually Bismark and ignore the Bowtie 2 or HISAT2 logs.

File search patterns

bowtie2:
  contents: "reads; of these:"
  exclude_contents:
    - bisulfite
    - HiC-Pro
  shared: true