CLC worcbench assembly

Question

[reza]

hi everyone how i can do denovo assembly (scoffold level) paired end sequencing data using CLC workbench? CLC do assembly in scoffolding level?

[Devon Ryan]

CLC is a commercial product, call them and ask.

[Whoknows]

Use CLC help manual.

Answer 1

[lakhujanivijay]

Hi Reza,

For a quick reference, look at page#404 of below pdf:

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/User_Manual.pdf

Yes, CLC will provide fasta format scaffold file.

[reza]

thanks a lot vijay. the number of scoffld created using CLC is more than other programs. is there any way to reduce numbers of scoffolds leading to bigger scoffolds?

[lakhujanivijay]

You're welcome. A high number of short length scaffolds is an indication of poor assembly. A high N50 and low number of contigs, relative to your expected number of chromosomes is ideal. Have a look at existing assemblies of closely related organisms if available to get an idea.

There are 2 ways to filter scaffolds of short lengths:

1. You can increase the threshold for min. contig length, see this screen shot:

2. You can first perform the assembly and later, filter the sequences by length. See this post.