Uses minimap2 to align sequences agains a reference databse.
Uses options '-ax splice -t 12 -k14 –secondary=no fa_file fq_in'
Usage
minimap2_align(
fq_in,
fa_file,
config,
outfile,
minimap2_args,
sort_by,
minimap2,
samtools,
threads = 1,
tmpdir
)Arguments
- fq_in
File path to the fastq file used as a query sequence file
- fa_file
Path to the fasta file used as a reference database for alignment
- config
Parsed list of FLAMES config file
- outfile
Path to the output file
- minimap2_args
Arguments to pass to minimap2, see minimap2 documentation for details.
- sort_by
Column to sort the bam file by, see
samtools sortfor details- minimap2
Path to minimap2 binary
- samtools
path to the samtools binary.
- threads
Integer, threads for minimap2 to use, see minimap2 documentation for details,
- tmpdir
Temporary directory to use for intermediate files. FLAMES will try to detect cores if this parameter is not provided.