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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

bowtie2 Map sequence reads to reference sequence
bowtie2build 从参考层层序创建领结2索引文件es
bowtie2inspect Inspect Bowtie 2 index files
bwaindex Create BWA indices from reference sequence
bwamem Map sequence reads to reference genome using BWA
align2cigar Convert aligned sequences to corresponding signatures in CIGAR format
cigar2align Convert unaligned sequences to aligned sequences using signatures in CIGAR format

Classes

BioMap Contain sequence, quality, alignment, and mapping data
Bowtie2AlignOptions Options to map reads to reference sequence
Bowtie2BuildOptions Contain options to create Bowtie 2 index files from reference sequences
Bowtie2InspectOptions Contain options to inspect Bowtie 2 index files
BWAIndexOptions Option set forbwaindex
BWAMEMOptions Option set forbwamem

Topics