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SUBLONG(1) User Commands SUBLONG(1)


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

Save mapping results in SAM format.

# number of CPU threads

-T <int>
Number of CPU threads used. 1 by default.

# others

Output version of the program.
Turn on the RNA-seq mode.

Refer to Users Manual for detailed description to the arguments.

February 2020 sublong 2.0.0+dfsg-1~bpo10+1