BWA

BWA (Burrows-Wheeler Aligner) [1] is a program that aligns short deep-sequencing reads to long reference sequences.

Running BWA in HPC

Request a compute node

srun --time=120 --pty --mem=8g /bin/bash

Load the module

module load bwa

Copy the file in FASTA format "rs_ch1.fas" from /usr/local/doc/BWA

cp /usr/local/doc/BWA/rs_ch1.fas .

Create a index for reference genome and follow the instructions at [1].

bwa index -p rsch1bwaidx -a bwtsw rs_ch1.fas

The descriptions of the options can be viewed by issuing command "bwa index"

output:

[bwa_index] Pack FASTA... 90.96 sec

[bwa_index] Construct BWT for the packed sequence...

[BWTIncCreate] textLength=5722412362, availableWord=414650000

[BWTIncConstructFromPacked] 10 iterations done. 99999994 characters processed.

[BWTIncConstructFromPacked] 20 iterations done. 199999994 characters processed.

...

[BWTIncConstructFromPacked] 640 iterations done. 5722412362 characters processed.

[bwt_gen] Finished constructing BWT in 640 iterations.

[bwa_index] 2900.83 seconds elapse.

[bwa_index] Update BWT... 16.04 sec

[bwa_index] Pack forward-only FASTA... 79.88 sec

[bwa_index] Construct SA from BWT and Occ... 898.36 sec

[main] Version: 0.7.12-r1039

[main] CMD: bwa index -p rsch1bwaidx -a bwtsw rs_ch1.fas

[main] Real time: 4028.271 sec; CPU: 3986.073 sec

You will also find rsch1bwaidx.amb rsch1bwaidx.ann rsch1bwaidx.bwt rsch1bwaidx.pac rsch1bwaidx.sa files.

References: