14 contigs recieved from SMRTportal using HGAP.3

Question

[komwit.s]

Hi,

I try to assembly my Lactobacillus genome in HGAP.3 using SMRTPortal. I set genome size about 3000000 bp and use coverage at 15x. I do not adjust any other parameter and I got 14 contigs as a result. The max contig length is 1,970,329. Sum of Contig Lengths is 3,111,026

Do you have any recommendation for adjusting the parameter to produce less contig than this? Hopefully you can give me some advice.

Polished Contigs 14
Adapter Dimers (0-10bp) 0.01%
Short Inserts (11-100bp) 0.0%
Number of Bases 829,596,363
Number of Reads 76,328
N50 Read Length 20,810
Mean Read Length 10,868
Mean Read Score 0.84
Mapped Reads 68,969
Mapped Read Length of Insert 4,333
Average Reference Length 222,207
Average Reference Bases Called 100.0%
Average Reference Consensus Concordance 99.98%
Average Reference Coverage 191.48

[Adrian Pelin]

I would just assemble it with something else and try and combine assemblies. With such a small amount of contigs, it shouldn't be too hard.

[GenoMax]

Tagging Dr. Hall: rhall

Answer 1

[gangireddy]

The first step is removal of contamination. have you checked for contamination and excluded the contaminant reads. If done. Then,

I don't know for sure. but I think input is around 280x.

try increasing minimum subread length such that

Total Number of Bases(filtered subreads)/genome_size around 100

then check

Total Number of Bases (preassembled reads) / genome_size = ?

and change the target genome coverage to obtained value.

Then play with assembler parameters ovlMinLen, ovl ErrorRate and mersize

[komwit.s]

I've solved the problem. Thank you for you suggestions.