[GenoMax]

No.

@luc is referring to DISCOVAR DeNovo which is an assembler meant for large genomes. It *requires* 2 x 250 bp reads which currently can only be produced by suitably equipped HiSeq 2500 (in the amount needed, so MiSeq practically does not count).

On a different note, DISCOVAR DeNovo also needs ~1 TB(+) of RAM to function well (e.g. you are going to use 500 million reads for assembly). You read that right!

[westerman]

The one time I tried out DISCOVAR DeNovo on a mammalian genome I had to borrow a 512 GB machine. As is all too typical for bioinformatics programs DISCOVAR at times took up all CPUs and at other times poked along using a single CPU. Relevant lines from the log file follow:

physical memory: 504.74 GB

using 708,777,836 reads
data extraction complete, peak mem = 260.85 GB
3.27 hours used extracting reads

back from buildReadQGraph
memory in use = 191.83 GB, peak = 405.28 GB

1 peak mem usage = 405.28 GB
2.42 minutes used loading stuff
2 peak mem usage = 405.28 GB
launching gap assemblies, mem usage = 179,701,415,936

now processing 411707 blobs
memory in use = 191.38 GB, peak = 405.28 GB

contig line N50: 46,487
scaffold line N50: 108,870
total bases in 1 kb+ scaffolds: 2,223,980,361
total bases in 10 kb+ scaffolds: 2,102,334,133
There are 708,777,836 reads of mean length 229.9 and mean base quality 34.3.
MPL1 = mean length of first read in pair up to first error = 199
(normal range is 175-225 for 250 base reads)
Estimated chimera rate in read pairs (including mismapping) = 0.46%.
genomic read coverage, using 1 kb+ scaffolds for genome size estimate: 73.3

peak mem usage = 405.28 GB, total time = 40.9 hours

Since I had mate-pairs I followed up DISCOVAR with BESST and got a very nice 2.4 GB genome with max of 9.7 MB, N50 of 1.8 MB with 375 scaffolds at N50 or greater.

My "go-to" default assembler (ABySS) only came up with a 2.4 GB genome with max of 2.6 MB, N50 of 230 KB with 2,689 scaffolds at N50 or greater. So DISCOVAR/BESST is a nice option if you have the reads.

[Alfonso-Rourich]

Ok, sorry, I thought that reads needed to be 250 bp long in total not 2x250 bp. We cannot afford (and it has no sense) a HiSeq but we could purchase a NextSeq and try to perform deNovo (besides RNA-Seq and resec. but for that there is no problem).

I work in a supercomputing center (but logically the sequencer will be used by a partner with background in genetics) so those computational requirements wouldn't be a problem. I'll have a look to DISCOVAR assembler.

Thank you, best regards