.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH ASSEMBLEPAIRS.PY "1" "May 2020" "AssemblePairs.py 0.6.0" "User Commands"
.SH NAME
AssemblePairs.py \- Assembles paired-end reads into a single sequence
.SH DESCRIPTION
usage: AssemblePairs.py [\-\-version] [\-h]  ...
.PP
Assembles paired\-end reads into a single sequence
.SS "help:"
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "subcommands:"
.IP
Assembly method
.TP
align
Assemble pairs by aligning ends.
.TP
join
Assemble pairs by concatenating ends.
.IP
reference
.IP
Assemble pairs by aligning reads against a reference database.
.IP
sequential
.IP
Assemble pairs by first attempting de novo assembly, then
reference guided assembly.
.SS "output files:"
.IP
assemble\-pass
.IP
successfully assembled reads.
.IP
assemble\-fail
.IP
raw reads failing paired\-end assembly.
.SS "output annotation fields:"
.IP
<user defined>
.IP
annotation fields specified by the \fB\-\-1f\fR or \fB\-\-2f\fR arguments.
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.