[boetsie]

I've just posted our new tool called GapFiller, which should be able to do this. See this thread;

http://seqanswers.com/forums/showthread.php?t=21493

Boetsie

Hi, I used the CLC-bio de novo assembly to analyze the Miseq 150bp PE data, and I have the 150 contigs. I also have the 170kb reference genome seq; I tried to use the IMAGE to close the gap, and it did not work for me. Can anyone suggest me how to close the gap? Thank you very much.

[sivasubramani]

I just completed reading the first(parent) post. There I got some doubts and where the data could have gone in different direction.
1. What is the kmer length you used for assembly. Becuase in such a high coverage data, if we use inappropriate kmer length(for example 23 for 72bp reads) of course you will get lot of false contigs and it will result you drive in wrong direction.
2. you din mention anywhere about the filtering and contamination check or quality filters. Because If it an alignment then you don need to worry about these factors but when you do denovo assembly with high coverage data each copy of read will affect your assembly.

better rather than using a default setup in clc workbench, you can try using different paraeters based on the data after filtering contaminated and low quality data.

Thanks

[stevebaeyen]

sivasubramani

Thank you for your excellent tips sivasubramani, but the problem is solved by now . I indeed used a very strict trimming, duplicate removal, etc. before doing de novo assembly wit a k-mer parameter sweep.