DOKK / manpages / debian 11 / abyss / abyss-fixmate.1.en

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.

set the qname to * [default]
do not alter the qname
print all alignments
print alignments that align to different contigs [default]
the minimal alignment size [1]
write properly-paired reads to this file
write the fragment size histogram to FILE
write the physical coverage to FILE
display verbose output
display this help and exit
output version information and exit
specify path of database repository in FILE
specify library NAME for sqlite
specify strain NAME for sqlite
specify species NAME for sqlite

Written by Shaun Jackman.

Report bugs to <>.

Copyright 2014 Canada's Michael Smith Genome Sciences Centre

December 2020 ABySS 2.2.5