Question: Tool for reducing contigs
1
gravatar for div
4.5 years ago by
div60
Banglore
div60 wrote:

Hi all,

I have MIRA assembled contigs of single end reads from Ion Torrent.

  • contigs number has to reduce
  • genome size has to retain
  • N50 value must increase.

This is the 3 points which we want to do in the post genome assembly project. If any one have experience please help me out and suggest which program i can use for this job??

Thank you in advance

 

ADD COMMENTlink modified 4.5 years ago by orange30 • written 4.5 years ago by div60
4
gravatar for biocyberman
4.5 years ago by
biocyberman800
Denmark
biocyberman800 wrote:

In my opinion, all three requirements lead to the question of merging/joining contigs. Provided that the de novo assembler has done its best, there would be no de novo method to achieve the goals. The way out is to improve sequencing part by increase sequencing depth,  sequencing quality, sequencing method, etc.

With that said, you can try trimming reads by quality/adapters,  or/and loosen up de novo assembly parameters to let reads/and contigs find more bridging reads to assemble. 

Update:

After the first writing of this answer, I found myself in need to do the similar work more frequently. And I found this tool SPAdes (http://bioinf.spbau.ru/spades) which works quite nicely for small genomes (and the tool aims at small genomes). It does error correction, de novo assembly, contig extension and scaffolding. I've also tried free versions of SSPACE and GAPFILL. Which also works alright, but only for contig extension. Still again, I did not manage to do in-depth verification to see if the contig extension step is actually doing it right and not introducing errors.  The only indication is that BUSCO (http://busco.ezlab.org/) output is better.  So if improving sequencing reads is not an option, I would recommend SPAdes and BUSCO. 

 

ADD COMMENTlink modified 3.8 years ago • written 4.5 years ago by biocyberman800
3
gravatar for Jeremy Leipzig
4.5 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

I rather like the straightforward commands you have given us. This process is called "finishing". 

http://www.cbcb.umd.edu/finishing/

ADD COMMENTlink written 4.5 years ago by Jeremy Leipzig18k
1
gravatar for spenagon
4.5 years ago by
spenagon10
Spain
spenagon10 wrote:

Try PAGIT: https://www.sanger.ac.uk/resources/software/pagit/

ADD COMMENTlink written 4.5 years ago by spenagon10

yeah I have already tried PAGIT but it is a tool for paired end reads....and my assemblies are from single end reads :)

 

ADD REPLYlink written 4.5 years ago by div60
1
gravatar for orange
4.5 years ago by
orange30
Korea, Republic Of
orange30 wrote:

try AHA or PBjelly2 or sspace-longread for scaffoding .

ADD COMMENTlink written 4.5 years ago by orange30

@ Orange...yeah definitely i ll try both...thank you..:)

ADD REPLYlink written 4.5 years ago by div60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1983 users visited in the last hour