Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
The Bowtie 2 module parses results generated by Bowtie 2, an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Please note that the Bowtie 2 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
Bowtie 2 logs are from
STDERR - some pipelines (such as Cluster Flow)
print the Bowtie 2 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 is 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 logs.
File search patterns
bowtie2: contents: "reads; of these:" exclude_contents: - bisulfite - HiC-Pro shared: true