GroupB aligner

Aligner created by GroupB Computational Biomedicine students.

Authors: Brynja Sigurpalsdottir, Hana Parizkova, Karthik Pattisapu, Modestas Filipavicius, Zhi Ye

Strategies used

• Genome Indexing: Burrows-Wheeler transform
• Seeding: FM-index; variable length and number of seeds; position of seed in the read chosen randomly
• Alignment: Semi-global dynamic-programming alingment with affine gap penalties; scoring as in bowtie2

Usage

Requires Python 3.7.1.

Run run_alignment.py.

Required arguments

• --fastq ... names of one or more FastQ files with reads to be aligned
• --genomeIndexDir ... directory where genome index is stored, or where it should be stored if we run indexing as well
• --outFile ... output file (in SAM format)
• --genomeFasta ... name of Fasta file with the genome sequence

Other basic arguments

• --runIndexing ... run also indexing of the genome; by default indexing is not run

Advanced arguments

• --overhang ... float value specifiying how large overhang over the length of the read will be taken into account when running DP alignment; default value 0.33, i.e. the alignment will be computed on a piece of genome of lenght 1.33*readLength
• --seedLength ... length of seeds in base pairs; default 10
• --numberOfSeeds ... number of seeds to be tried for each read; default value 3

Examples

• Basic usage, genome index already present: python run_alignment.py --fastq FILE.FASTQ --genomeIndexDir GENOMEDIR --genomeFasta GENOME.FASTA --outFile OUTFILE
• If we want to run indexing of genome as well: python run_alignment.py --fastq FILE.FASTQ --genomeIndexDir GENOMEDIR --genomeFasta GENOME.FASTA --outFile OUTFILE --runIndexing