sublong - long-read aligner that is designed based on
seed-and-vote
sublong [options] -i <index_name> -r
<input> -o <output>
## 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.