Alignment

Map reads to reference sequence(s)

Align sequence reads to reference sequences using the Bowtie 1 (bowtie) and Bowtie 2 (bowtie2) alignment functions. Bowtie 1 is geared toward aligning relatively short reads (up to 50 bp). Bowtie 2 is more 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.

Functions

bowtieMap short reads to reference sequence using Burrows-Wheeler transform
bowtiebuildGenerate index using Burrows-Wheeler transform
bowtie2Map sequence reads to reference sequence
bowtie2buildCreate Bowtie 2 index files from reference sequences
bowtie2inspectInspect Bowtie 2 index files
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

Topics

Visualize and Investigate Sequence Read Alignments

Use NGS Browser to visualize and investigate sequence read alignments and feature annotations