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ABYSS-FIXMATE(1) User Commands ABYSS-FIXMATE(1)

NAME

abyss-fixmate - Fill the paired-end fields of SAM alignments

SYNOPSIS

abyss-fixmate [OPTION]... [FILE]...

DESCRIPTION

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

AUTHOR

Written by Shaun Jackman.

REPORTING BUGS

Report bugs to <abyss-users@bcgsc.ca>.

COPYRIGHT

Copyright 2014 Canada's Michael Smith Genome Sciences Centre
September 2019 abyss-fixmate (ABySS) 2.2.3