Closed Hans-zhao831 closed 3 years ago
Hi Hans,
Best,
Alex
Hi Alex (@adigenova),
On the topic of coverage, we have ~30X of short reads and ~40X of ONT reads (N50 ~30Kb) for a genome that is the similar size of human. Is it better to run on M mode or D mode?
Was trying on the D mode but got this error message (see below). Not sure what the problem is.
export MALLOC_PER_THREAD=1
/wengan/wengan-v0.2-bin-Linux/bin/DiscovarExp READS="Illumina/203_tursiops_unclass_Clean_R_1.fastq.gz,Illumina/203_tursiops_unclass_Clean_R_2.fastq.gz" OUT_DIR=/tmp/asm_wenganDD NUM_THREADS=32 2> asm_wenganD.Disco_denovo.err > asm_wenganD.Disco_denovo.log
asm_wenganD.mk:4: recipe for target 'asm_wenganD.contigs-disco.fa' failed
make: *** [asm_wenganD.contigs-disco.fa] Error 1
In asm_wenganD.Disco_denovo.log
1: 60 bases , 31 quals
2: 60 bases , 31 quals
See inconsistent base/quality lengths in Illumina/203_tursiops_unclass_Clean_R_1.fastq.gz or Illumina/203_tursiops_unclass_Clean_R_2.fastq.gz
Not sure what this mean. We did the standard QC for our short reads.
Would appreciate your advice! Thanks Zih-Hua
Hi Zih-Hua,
Is it better to run on M mode or D mode? Wengan achieves better results with the D mode, but the D mode requires more memory than the other ones. For a 3Gb genome at 60X short read coverage the D mode need about 600Gb, for lower coverage ~30X, it would require about 300Gb.
Regarding the error message, DiscovarDenovo (Disco for short) is complaining that there are short-reads in your dataset with inconsistencies in the lengths of quality and bases (probably a corrupt fastq file). My recommendation is to give the raw short-reads as input to Wengan, because Disco error-correct the short-read data using sophisticated algorithms that are more convenient than just trimming reads based on single read qualities. Additionally. reads shorter than 60bp are not supported by Disco and also stop its execution. You can check that your reads are longer than 60bp using fastp for instance. Best Alex
Dear Alex,
Thanks for the reply. Just one quick question about trimming the reads. Our reads are generated from NovoSeq, so there is poly-G tail for each read. I guess I would still need to trim it before putting the reads to Wengan?
Thanks. Zih-Hua
Yes, you can trim that tail, but be sure that all the reads are longer than 60bp. Best,
Alex
Hello, I am trying to assemble a plant genome using different genome assembly software. I am very interested in wengan, but I have some problems.