.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH FSA_ASSEMBLE "1" "July 2020" "Constructs contigs from filtered overlaps and corrected reads." "User Commands"
.SH NAME
fsa_assemble \- Constructs contigs from filtered overlaps and corrected reads
.SH SYNOPSIS
.B fsa_assemble
[\fI\,options\/\fR] \fI\,filterd_overlaps\/\fR
.SH DESCRIPTION
Constructs contigs from filtered overlaps and corrected reads.
.SH OPTIONS
.HP
\fB\-\-min_length\fR=\fI\,INT\/\fR
.IP
minimum length of reads
default: 0
.HP
\fB\-\-min_identity\fR=\fI\,DOUBLE\/\fR
.IP
minimum identity of overlaps
default: 0
.HP
\fB\-\-min_aligned_length\fR=\fI\,INT\/\fR
.IP
minimum aligned length of overlaps
default: 0
.HP
\fB\-\-min_contig_length\fR=\fI\,INT\/\fR
.IP
minimum length of contigs
default: 500
.HP
\fB\-\-read_file\fR=\fI\,STRING\/\fR
.IP
read filename
default: ""
.HP
\fB\-\-overlap_file_type=\fR"|m4|m4a|paf|ovl"
.IP
overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON.
default: ""
.HP
\fB\-\-output_directory\fR=\fI\,STRING\/\fR
.IP
directory for output files
default: "."
.HP
\fB\-\-select_branch=\fR"no|best"
.IP
selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch
default: "no"
.HP
\fB\-\-thread_size\fR=\fI\,INT\/\fR
.IP
number of threads
default: 1
.HP
\fB\-\-dump\fR=\fI\,INT\/\fR
.IP
for testing, dump intermediate files
default: 0
.HP
\fB\-\-run_mode\fR=\fI\,INT\/\fR
.IP
for testing
default: 4
.HP
\fB\-\-lfc\fR
.IP
deprecated, for testing
.HP
\fB\-\-remove_chimer\fR
.IP
deprecated, remove chimer node
.PP
Usage: fsa_assemble [options] filterd_overlaps
.IP
filterd_overlaps
.IP
input filename
.HP
\fB\-\-min_length\fR=\fI\,INT\/\fR
.IP
minimum length of reads
default: 0
.HP
\fB\-\-min_identity\fR=\fI\,DOUBLE\/\fR
.IP
minimum identity of overlaps
default: 0
.HP
\fB\-\-min_aligned_length\fR=\fI\,INT\/\fR
.IP
minimum aligned length of overlaps
default: 0
.HP
\fB\-\-min_contig_length\fR=\fI\,INT\/\fR
.IP
minimum length of contigs
default: 500
.HP
\fB\-\-read_file\fR=\fI\,STRING\/\fR
.IP
read filename
default: ""
.HP
\fB\-\-overlap_file_type=\fR"|m4|m4a|paf|ovl"
.IP
overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON.
default: ""
.HP
\fB\-\-output_directory\fR=\fI\,STRING\/\fR
.IP
directory for output files
default: "."
.HP
\fB\-\-select_branch=\fR"no|best"
.IP
selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch
default: "no"
.HP
\fB\-\-thread_size\fR=\fI\,INT\/\fR
.IP
number of threads
default: 1
.HP
\fB\-\-dump\fR=\fI\,INT\/\fR
.IP
for testing, dump intermediate files
default: 0
.HP
\fB\-\-run_mode\fR=\fI\,INT\/\fR
.IP
for testing
default: 4
.HP
\fB\-\-lfc\fR
.IP
deprecated, for testing
.HP
\fB\-\-remove_chimer\fR
.IP
deprecated, remove chimer node