Shayan Doust pushed to branch master at Debian Med / graphbin
Commits: 8d66d9ae by Shayan Doust at 2020-07-16T17:21:08+01:00 Write manpage - - - - - 2 changed files: - + debian/graphbin.manpages - + debian/mans/graphbin.1 Changes: ===================================== debian/graphbin.manpages ===================================== @@ -0,0 +1 @@ +debian/mans/*.1 ===================================== debian/mans/graphbin.1 ===================================== @@ -0,0 +1,48 @@ +.TH GRAPHBIN "1" "July 2020" "graphbin" "User Commands" +.SH NAME +graphbin \- refined binning of metagenomic contigs using assembly graphs +.SH SYNOPSIS +usage: graphbin [\fI\,-h\/\fR] \fB\-\-assembler\fR \fI\,ASSEMBLER\/\fR \fB\-\-graph\fR \fI\,GRAPH\/\fR [\-\-paths \fI\,PATHS\/\fR] +\fB\-\-binned\fR \fI\,BINNED\/\fR \fB\-\-output\fR \fI\,OUTPUT\/\fR [\-\-prefix \fI\,PREFIX\/\fR] +[\-\-max_iteration \fI\,MAX_ITERATION\/\fR] +[\-\-diff_threshold\fI\, DIFF_THRESHOLD\/\fR] +.SH DESCRIPTION +.PP +GraphBin is a metagenomic contig binning tool that makes use of +the contig connectivity information from the assembly graph to bin contigs. It +utilizes the binning result of an existing binning tool and a label +propagation algorithm to correct mis\-binned contigs and predict the labels of +contigs which are discarded due to short length. +.SS "optional arguments:" +.TP +\fB\-h\fR, \fB\-\-help\fR +show this help message and exit +.TP +\fB\-\-assembler\fR ASSEMBLER +name of the assembler used (SPAdes, SGA or MEGAHIT). +GraphBin supports Flye, Canu and Miniasm long\-read +assemblies as well. +.TP +\fB\-\-graph\fR GRAPH +path to the assembly graph file +.TP +\fB\-\-paths\fR PATHS +path to the contigs.paths file +.TP +\fB\-\-binned\fR BINNED +path to the .csv file with the initial binning output +from an existing tool +.TP +\fB\-\-output\fR OUTPUT +path to the output folder +.TP +\fB\-\-prefix\fR PREFIX +prefix for the output file +.TP +\fB\-\-max_iteration\fR MAX_ITERATION +maximum number of iterations for label propagation +algorithm. [default: 100] +.TP +\fB\-\-diff_threshold\fR DIFF_THRESHOLD +difference threshold for label propagation algorithm. +[default: 0.1] View it on GitLab: https://salsa.debian.org/med-team/graphbin/-/commit/8d66d9aec21603c40f2181165cd052dc4cd6f648 -- View it on GitLab: https://salsa.debian.org/med-team/graphbin/-/commit/8d66d9aec21603c40f2181165cd052dc4cd6f648 You're receiving this email because of your account on salsa.debian.org.
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