OmicSoft Aligner

Whitepaper discussing the technique of aligning next generation sequencing (HTS) data.

OSA is Omicsoft's read aligner designed for high performance alignment of short or long reads to reference libraries (genomes or transcriptomes).

 Key features of OSA:
1. High performance for both single end alignment and paired end alignment. Works on reads with 17-65536 nucleotides.
2. For Illumina reads (17nt or longer), allow any number of mismatches and a single indel in the reads. Can identify and report all available alignments in the genome with specified mismatches/indel.
3. For long reads (e.g. 454 reads or PacificBio reads), allow any number of mismatches and indels in the reads. Use banded Smith-Waterman to find the optimal alignment.
4. Directly align RNA-Seq reads to genome by considering both known and novel exon junctions
5. Directly align fusion reads: reads spliced by two different genes or genomic regions
6. Automatic quality based trimming
7. Automatic adapter trimming
8. Support all common input formats (.fasta; .fastq; .qseq; .sff); directly support .gzip files allowing savings in file space
9. Support multiple threads