clc genome finishing module auto join tool

[Kyubi]

Hi everyone

I recently used the clc genome finishing module autojoin tool to assemble my contigs. the tool reduced the number of contigs i had from 170 to 30, i also found that 1 of the contigs spanned a plasmid which was expected. i mapped reads to my joined contigs and had 94% of my reads mapping to the assembled contigs. i wish to know if there is a method for checking the quality of assembling my contigs ?? as i wish to know whether what i did to join contigs was correct

In order to assemble my contigs. I firstly used the join contigs tool which joined about 11 contigs, then i took the data and used the map contigs to a reference ( i have a reference thats similer to my contigs, this joined about 121 contigs and then i used map long reads to contigs tool and this joined 2 contigs.

just an added note: i am using Iontorrant PGM 400bp kit

thanks

[Sergioo]

Hello Kyubi,
Did you came up with a solution to your joined contigs?
If I remember, the "contig joining tool" of CLC is still in Beta version, thus somehow not yet sure!
If it is not yet late, I'd recommend you to join contigs manually in CLC! in 1 day, you can drastically reduce the number of your initial contigs and you will be confident of the work done.
All the best,

[Kyubi]

Hay sorry for the late reply,

i think the CLC genome finishing module would be good in reducing the number of contigs. My initial DeNovo was not done well and by the time i realized this i ran out of the CLC genome finishing module trial.

if i had a chance of doing the samples again i would use cisa to combine my torrant asembled contigs with clc assembled contigs and then join manually using clc genome finishing module.

I managed to reduce the number of contigs by using CISA on my samples then i used geneious software to further reduce my contigs.
then i mapped reads onto my contigs and collected the unmapped reads using clc, then i used that to further extend and join contigs on geneious.

i then scaffolded my contigs using contiguator.

The % of nucleotides mapped onto my scaffolded sequence was 98% (you can get this value from clc after mapping reads). This means that the gaps i currently have are most likely going to be small enough to be filled in using sanger sequencing. i have around 32 gaps.