GASE - Generic Aligner for Seed-and-Extend

GASE is a DNA read aligner that allows to use different combinations of seeding and extension algorithms. GASE is implemented by extending BWA (version 0.7.13) developed by Heng Li. Currently, GASE supports 4 kinds of seeding techniques:

1. All the SMEMs (super-maximal exact matches) in a DNA read (all-SMEM). This is same as SMEM seeding in BWA-MEM.
2. Only the non-overlapping SMEMs (nov-SMEM).
3. Fixed length seeds with no mismatch.
4. Fixed length seeds with at most 1 mismatch.

Currently re-seeding is only available for all-SMEM. The reseeding algorithm is same as in BWA-MEM. Three different kind of seed extension techniques can be used:

1. Global alignment
2. Local alignment
3. BLAST-like seed extension

To compile GASE, run make. To use GASE we first need to build the index by executing the following command:

gase index <ref.fa>

This commands builds the FMD index which is the same as the one used in BWA. To align DNA reads use the following command:

gase gase_aln [options] <ref.fa> <reads.fastq>

Fo all the available alignment options type gase gase_aln. To test different seeding algorithms only, use the following command:

gase fastmap [options] <ref.fa> <reads.fastq>

For the available options type in gase fastmap.

Feel free to conatact Nauman Ahmed: [email protected] for any issues or bugs.