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m4merg 08-14-2014 12:51 AM

1000 Genomes analysis workflow
I wonder was performed alignment on contigs in 1000 Genome project. I wanted to check frequency of huge insertions, but it is not possible to do if the alignment was done only on reference genome 37p13. I checked files on ftp server and didnt found anything that could help me. I've read documentation and as i understood right alignment was preformed only on reference. So I just want to get sure that i got everything right.

Thx in advance.

m4merg 08-15-2014 04:49 AM

That's answer from their support if someone interested in:

You are correct that the sequence reads were mapped to reference genome; the
project did not produce a de novo assembly from the reads.

The project did use several algorithms (cortex, SGA, and GATK haplotype caller)
that are based on reference free concepts for calling and validating variants;
however no de novo assembly was produced in the process.

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