.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH RUNMETABAT.SH "1" "May 2020" "runMetaBat.sh 2.15" "User Commands"
.SH NAME
runMetaBat.sh \- Wrapper for MetaBAT
.SH DESCRIPTION
.B 
runMetaBat.sh
\fI <select metabat options> assembly.fa sample1.bam [ sample2.bam ...]\fR
.SH OPTIONS
You can specify any metabat options EXCEPT:
.HP
\fB\-i\fR \fB\-\-inFile\fR
.HP
\fB\-o\fR \fB\-\-outFile\fR
.HP
\fB\-a\fR \fB\-\-abdFile\fR
.PP
Also for depth calculations stage only, you can set the following environmental variables:
.TP
PCTID=97
\fB\-\-\fR reads below this threshold will be discarded
.TP
BADMAP=0
\fB\-\-\fR output the discarded reads to a sub directory
.TP
MINDEPTH=1.0
\fB\-\-\fR require contigs to have this minimum depth to be output
.PP
For full metabat options: metabat2 \fB\-h\fR
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.