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Will it be fine if the benchmarking of an assembler/aligner is performed using a single chromosome of Human

Hi Everyone

I have been reading several benchmarking papers and I realized how much computational resources and time it must have cost for all the chromosomes we have in the human reference genome. Wouldn't it be a more principled approach to use the longest and the shortest chromosome to use in benchmarking studies of aligners/assemblers ? If not why.

assembly sequence alignment genome next-gen
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updated by JC JC • written by rohitsatyam102 rohitsatyam102

If you only had sequence data from those two chromosome then yes. You could artificially retrieve the data that is aligning to just those particular chromosome and then use it (after doing an alignment to the full genome).

Keep in mind this would only be appropriate for the synthetic purpose of benchmarking.

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written by GenoMax GenoMax

No I have WGS data. So it covers the entire genome.

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written by rohitsatyam102 rohitsatyam102

Correct. But you can pull out reads from that data that just align to two chromosomes and do what I mentioned above for benchmarking.

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written by GenoMax GenoMax

1 answer

No, because aligners also deal with multiple mapping issues, the realistic way is to use the full genome.

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written by JC JC

Any thoughts on the assembler's side.

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written by rohitsatyam102 rohitsatyam102

What do you mean? For assemblers is common to benchmark using different library sizes with several total reads sizes.

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written by JC JC

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