https://manual.genomeview.org/index.php?action=history&feed=atom&title=Recipe_to_align_reads 2026-05-16T02:32:50Z Revision history for this page on the wiki MediaWiki 1.35.6 https://manual.genomeview.org/index.php?title=Recipe_to_align_reads&diff=9963&oldid=prev 2013-10-17T22:54:34Z

<p>Created page with &quot;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...&quot;</p> <p><b>New page</b></p><div>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.<br /> <br /> You need:<br /> # a reference genome in FASTA format (reference.fasta)<br /> # read data in FASTQ format (reads_1.fastq and reads_2.fastq)<br /> # [http://sourceforge.net/projects/bio-bwa/files/ recent version of BWA] (a short read aligner). <br /> <br /> At the time of writing the most recent version of BWA is 0.7.5a<br /> <br /> == Step by step instructions ==<br /> 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.<br /> <br /> <br /> <br /> Build BWA index for the reference<br /> <br /> bwa index reference.fasta<br /> <br /> Align reads to the reference genome<br /> <br /> bwa mem reference.fasta reads_1.fastq reads_2.fastq &gt; alignment.sam<br /> <br /> 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:<br /> <br /> bwa mem reference.fasta reads.fastq &gt; alignment.sam<br /> <br /> <br /> You can visit the [http://bio-bwa.sourceforge.net/bwa.shtml BWA webpage] for more information and options</div>

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