Recipe to align reads

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This recipe will help you align reads to a reference genome. This is merely an example of one possible protocol with one alignemnt program. There are many more available.

You need:

  1. a reference genome in FASTA format (reference.fasta)
  2. read data in FASTQ format (reads_1.fastq and reads_2.fastq)
  3. recent version of BWA (a short read aligner).

At the time of writing the most recent version of BWA is 0.7.5a

Step by step instructions

These instructions need to be run in a terminal. To the best of our knowledge, BWA is only available for Unix based platforms like OS X and Linux.

Build BWA index for the reference

bwa index reference.fasta

Align reads to the reference genome

bwa mem reference.fasta reads_1.fastq reads_2.fastq > alignment.sam

Reads_1.fastq and reads_2.fastq indicate the two files that have the first and second read in a pair. If you data is not paired end sequencing the latter command would look like this:

bwa mem reference.fasta reads.fastq > alignment.sam

You can visit the BWA webpage for more information and options