Rationale and background
BWA Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. This instance of BWA works with paired-end sequencing reads. You can use BWA mem to align 70bp-1Mbp query sequences with the BWA-MEM algorithm, and to index and map Illumina reads (70-100bp) to a reference sequence.
A CyVerse account (Register for a CyVerse account at https://user.cyverse.org/).
An up-to-date Java-enabled web browser. (Firefox recommended. If you wish to work with your own large datasets and upload them using iCommands, Chrome is not suitable due to its issues in utilizing 64-bit Java.)
This tutorial uses the test data that is stored in the Data Store at Community Data > iplantcollaborative > example_data > bwa
- Use 10K_SRR192294_1.fastq for Left_Read file and 10K_SRR192294_2.fastq (2.4M) for Right_Read file
- Select a reference genome from the list - Brachypodium distachyon (line Bd21) v1
- All other parameters remain in their default state
Expect a SAM file named after the input files as output. For the test case, the output file is 10K_SRR192294_1.fastq-10K_SRR192294_2.fastq.sam (4.8M)