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Alignment

Map reads to reference sequence(s)

Align sequence reads to reference sequence(s) using the Bowtie alignment algorithm. Bowtie is a fast and memory-efficient aligner that uses an FM index based on the Burrows-Wheeler Transform (BWT) for alignment purposes. Use bowtiebuild to generate the index required for bowtie, and use bowtie to run the aligner.

Functions

bowtieMap short reads to reference sequence using Burrows-Wheeler transform
bowtiebuildGenerate index using Burrows-Wheeler transform
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

Topics

Visualize and Investigate Sequence Read Alignments

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

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