abyss-fixmate - Fill the paired-end fields of SAM alignments
abyss-fixmate [OPTION]... [FILE]...
Write read pairs that map to the same contig to the file SAME.
Write read pairs that map to different contigs to stdout. Alignments may be
in FILE(s) or standard input.
- Options:
- --no-qname
- set the qname to * [default]
- --qname
- do not alter the qname
- --all
- print all alignments
- --diff
- print alignments that align to different contigs [default]
- -l,
--min-align=N
- the minimal alignment size [1]
- -s,
--same=SAME
- write properly-paired reads to this file
- -h,
--hist=FILE
- write the fragment size histogram to FILE
- -c,
--cov=FILE
- write the physical coverage to FILE
- -v, --verbose
- display verbose output
- --help
- display this help and exit
- --version
- output version information and exit
- --db=FILE
- specify path of database repository in FILE
- --library=NAME
- specify library NAME for sqlite
- --strain=NAME
- specify strain NAME for sqlite
- --species=NAME
- specify species NAME for sqlite
Written by Shaun Jackman.
Report bugs to <abyss-users@bcgsc.ca>.
Copyright 2014 Canada's Michael Smith Genome Sciences Centre