What is a BWA index?
BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.
Table of Contents
What is a BWA index?
BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.
What does BWA MEM output?
The BWA-MEM algorithm performs local alignment. It may produce multiple primary alignments for different part of a query sequence. This is a crucial feature for long sequences. However, some tools such as Picard’s markDuplicates does not work with split alignments.
What does BWA MEM stand for?
Maximal Exact Match
The mem option stands for Maximal Exact Match. When bwa mem begins its alignment process for a particular read, the first thing it does is look for a long substring that matches the reference exactly and which can’t be extended to a longer match at either end – that is, it finds a maximal exact match.
What is the difference between BWA and BWA MEM?
BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.
How do you align with BWA?
Step 1: Index the reference database file that comprises 59 genomes. Step 2: Use BWA-MEM to align paired-end sequences. Briefly, the algorithm works by seeding alignments with maximal exact matches (MEMs) and then extending seeds with the affine-gap Smith-Waterman algorithm (SW). Step 3: Convert sam file to bam file.
What is BWA sequencing?
BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence, except for disallowing gaps close to the end of the query.
How does BWA aligner work?
BWA supports paired-end mapping. It first finds the positions of all the good hits, sorts them according to the chromosomal coordinates and then does a linear scan through all the potential hits to pair the two ends.
How do you cite the BWA aligner?
The short read alignment component (bwa-short) Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760.
How do you cite BWA MEM?
If you decide to use bwa-mem, please cite: “Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM.
How long does BWA take to run?
Useful Information
| total # of sequences | used time for 4 CPUs | |
|---|---|---|
| large_1.fastq | 10,174,715 | ~ 35 minutes |
| large_2.fastq | 10,174,715 | |
| large.fasta | 592,593 | ~ 5.5 minutes |
How many iterations does BWA index do?
10 iterations
Building the hg19 BWA index. The hg19 genome reference index was built on a training linux Mint 17.3 virtual machine with 6GB RAM. The process was quite long abut resulted in the expected files. [BWTIncConstructFromPacked] 10 iterations done.
How does BWA alignment work?