.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH SUBLONG "1" "February 2020" "sublong 2.0.0+dfsg-1~bpo10+1" "User Commands"
.SH NAME
sublong \- long-read aligner that is designed based on seed-and-vote
.SH USAGE
.PP
sublong [options] \fB\-i\fR <index_name> \fB\-r\fR <input> \fB\-o\fR <output>
.PP
## Mandatory arguments:
.TP
\fB\-i\fR <string>
Base name of the index. The index must be built as a full index
and has only one block.
.TP
\fB\-r\fR <string>
Name of an input read file. Acceptable formats include gzipped
FASTQ and FASTQ (automatically identified).
.TP
\fB\-o\fR <string>
Name of an output file in BAM format.
.PP
## Optional arguments:
# input reads and output
.TP
\fB\-\-SAMoutput\fR
Save mapping results in SAM format.
.PP
# number of CPU threads
.TP
\fB\-T\fR <int>
Number of CPU threads used. 1 by default.
.PP
# others
.TP
\fB\-v\fR
Output version of the program.
.TP
\fB\-X\fR
Turn on the RNA\-seq mode.
.PP
Refer to Users Manual for detailed description to the arguments.