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
- Visualize NGS Data Using Genomics Viewer App
Use the Genomics Viewer app to view NGS alignment data for single nucleotide variation in cytochrome p450 gene.
- Bioinformatics Toolbox Software Support Packages
Download and install Bioinformatics support packages for NGS workflows.