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BWA: Importing a third-party indexed genome
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4.5 years ago
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I guess my question is going to sound pretty basic, but nevertheless I need to understand clearly how to use bwa .

I am not able to run a bwa indexing of the GRCh38 reference genome on my laptop, due to memory usage requirements (~5GB needed, according to the bwa man page).

The 1000 Genomes Project offers what seems to be an indexed version of it on its FTP servers.

Can I download the entire directory and use bwa locally for my alignments, without running a brand new indexing?

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If you are not able to create an index then you would not be able run the alignments either since that also typically requires 5G of memory. See this note from Heng.

But the answer for your original question is yes. It is possible to use pre-formatted indexes that you get from someplace else.

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Try the igenomes of illumina

http://support.illumina.com/sequencing/sequencing_software/igenome.html

Huge zipped files but contain all the sequences you may need, indexed (for bwa, bowtie etc.) or not (chr fasta and full genomic fasta files)

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