We have sequenced whole genome of fungi using 3K (250bp), 8K (250bp) and shotgun (450bp) library. How can we assemble these data up to scaffold level using SOAPdenovo2? Is there any good assembler?
ABySS is not bad, and it doesnt' have much config to do compared to SOAPdenovo2 and you can use single end, pair end and mate pair libraries at the same time
You can run something like:
abyss-pe k=25 n=10 name=ecoli lib='lib1 lib2' \
lib1='lib1_1.fa lib1_2.fa' lib2='lib2_1.fa lib2_2.fa' \
se='se1.fa se2.fa' \
mp1='mp1_1.fa mp1_2.fa' mp2='mp2_1.fa mp2_2.fa'
Where
k is the kmer size as usual
se=' ' defines the single end files (e.g. FASTA)
lib=' ' defines the paired end libraries with name lib1 and lib2
mp =' ' lists mate-pair libraries if you have
More info here
https://github.com/bcgsc/abyss#abyss
http://seqanswers.com/wiki/ABySS
Thanks for your reply. Further, I have problem regarding the annotation of whole genome. The reference fungi has approximately 10,000 to 11, 000 genes but when I am doing gene annotation using Augustus , it showing only 7,500 genes. What could be the reason?
Is the reference sequence from the same organism? The closer they are related the better will be the prediction in theory.
How many scaffolds did you get after assembly? You may lose some info in regions poorly covered by sequencing.
How old is the annotation of the reference? How well curated is the reference? No prediction method is perfect, and specially when you start to deal with hypothetical proteins.
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