minimap2_align {FLAMES} | R Documentation |
Uses minimap2 to align sequences agains a reference databse.
Uses options "-ax splice -t 12 -k14 –secondary=no fa_file
fq_in
"
minimap2_align( minimap2_prog_path = NULL, fa_file, fq_in, sam_out, no_flank = FALSE, bed12_junc = NULL )
minimap2_prog_path |
Absolute path to the directory containing minimap2 |
fa_file |
Path to the fasta file used as a reference database for alignment |
fq_in |
File path to the fastq file used as a query sequence file |
sam_out |
File path to the output SAM file |
no_flank |
Boolean; used if studying SIRV, to tell minimap2 to ignore additional bases |
bed12_junc |
file path to the gene annotations in BED12 format. If specified, minmap2 prefers splicing in annotations. |
file path to the given output BAM file, bam_out