Programs for [de novo] assembly - human genome

Question

[iowa69]

Hello guys,

I have always worked with bacterial genomes. Now I have to map sequences to reference human genome first and then to de novo assemble that. Illumina reads, shotgun human wgs.

What are the best tools for doing that? (32 cores, 64Gb of RAM platform, 1TB SSD)

Thanks!

[GenoMax]

32 cores, 64Gb of RAM platform, 1TB SSD

That will not be sufficient for de novo assembly of human data. You can use it to align the data to a reference. Depending on the size and amount of your data upwards of a TB of RAM may be needed for de novo assembly.

[iowa69]

Thanks for the reply,

Which program do you suggest to use to align/map the reads to reference?

What is the best tool for [trying] denovo assembly of human genome? I can use my university server (512GB RAM) for that.

Thanks again.

[WouterDeCoster]

For alignment, use bwa mem

[colindaven]

For assembly, try soapdenovo2. Expect very poor results if you don't have long range info such as mate pairs/long jumping distance, Hi-C, long reads pacbio/ ONT reads or similar.

Also, check out a couple of nature reviews in genetics papers on getting a good idea on the differences between mapping and assembly, which are fundamental.