Which Flash output file do you use in Soap denovo assembly

Question

[mafireyi]

I am trying to use Soap Denovo for my assembly. I first trimmed my reads with trimmomate and used Flash to merge reads. Flash outputs 4 output files. Which ones would I use as inputs for Soap denovo. Should I use the out.extendedFrags.fastq or should I include the out.notCombined ones too?

Thanks

Answer 1

[thackl]

Use out.extendedFrags.fastq for graph assembly with large k-mer size. You can use out.notCombined for scaffolding only (SOAP config: asm_flags = 2 I guess)

[mafireyi]

Thanks, will it be possible to get a complete assembly if i just use the graph assembly with asm_flags = 3. below is my config file for the pair end library

max_rd_len=100

[LIB]

name = Hiseq14

avg_ins=200

reverse_seq=0

asm_flags=3

rd_len_cutoff=100

rank=1

pair_num_cutoff=3

map_len=32

q1=/scratch/sysusers/godwin/GuavaGenome/Hiseq_Run14_150313/Sample_Guava_IT2_350/out.extendedFrags.fastq

Will that work? Sorry, I am quite new to Soap

[thackl]

Yes, that should be enough. However, I'm not entirely sure, what SOAP will do about scaffolding with only a single end library. My guess: not a lot ;).

I might be a good idea to add the trimmed but not flashed libraries as scaffold-only libraries (asm_flags = 2) to your config.