Alignment

Map reads to reference sequences

Align sequence reads to reference sequences using various functions. Bowtie 2 (bowtie2) is suitable for reads longer than 50 bp and provides several benefits including single- and paired-end reads support, local and end-to-end alignment support, and gapped alignment with affine penalties. The Burrows-Wheeler Alignment BWA (bwamem) is suitable for aligning 70 bp-1 Mbp query sequences. It works by seeding alignments with maximal exact matches and extending seeds with the affine-gap Smith-Waterman algorithm.

Functions

bowtie2Map sequence reads to reference sequence
bowtie2buildCreate Bowtie 2 index files from reference sequences
bowtie2inspectInspect Bowtie 2 index files
bwaindexCreate BWA indices from reference sequence
bwamemMap sequence reads to reference genome using BWA
align2cigarConvert aligned sequences to corresponding signatures in CIGAR format
cigar2alignConvert unaligned sequences to aligned sequences using signatures in CIGAR format

Classes

BioMapContain sequence, quality, alignment, and mapping data
Bowtie2AlignOptionsOptions to map reads to reference sequence
Bowtie2BuildOptionsContain options to create Bowtie 2 index files from reference sequences
Bowtie2InspectOptionsContain options to inspect Bowtie 2 index files
BWAIndexOptionsOption set for bwaindex
BWAMEMOptionsOption set for bwamem

Topics