Split sequencing reads by mapping them to multiple references simultaneously
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
reads:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
index:directory
Directory to place generated index
*
primary_ref:file
Path to the primary reference
other_ref_names:list
List of other reference ids apart from the primary
other_ref_paths:list
Path to other references paths corresponding to “other_ref_names”
only_build_index:string
true = only build index; false = mapping
index
bbsplit:directory
Directory with index files
bbsplit
primary_fastq
*primary*fastq.gz:file
Output reads that map to the primary reference
*primary*fastq.gz
all_fastq
*fastq.gz:file
All reads mapping to any of the references
*fastq.gz
stats
*txt:file
Tab-delimited text file containing mapping statistics
*.txt
log
*.log:file
Log file
*.log
versions
versions.yml:file
File containing software versions
versions.yml
BBMap is a short read aligner, as well as various other bioinformatic tools.
