NAME¶

USAGE¶

## Mandatory arguments:

-i <string>

Base name of the index. The index must be built as a full index and has only one block.

-r <string>

Name of an input read file. Acceptable formats include gzipped FASTQ and FASTQ (automatically identified).

-o <string>

Name of an output file in BAM format.

## Optional arguments: # input reads and output

--SAMoutput

Save mapping results in SAM format.

# number of CPU threads

-T <int>

Number of CPU threads used. 1 by default.

# others

-v

Output version of the program.

-X

Turn on the RNA-seq mode.

Refer to Users Manual for detailed description to the arguments.