Question: PacBio long read error correction tools
0
gravatar for freddiejung
17 months ago by
freddiejung30
Japan
freddiejung30 wrote:

Dear all,

in my previous post (https://www.biostars.org/p/303214/#303734), some people suggested that it's better to correct errors in log reads from PacBio sequel using short reads from illumina ahead of the genome assembly.

I happened to find that the assembly with only short reads contains lots of mis-assembled loci. The assembled sequences did not match FISH data. Currently we suspect that the extremely similar repeated sequences dispersed among the genome caused the mis-assembly.

In this case, I felt that error-correcting software would not work well like LoRDEC or HALC that needs the assembly derived from short reads as input. Is this right?

If so, what kind of software is better to correct errors?

ADD COMMENTlink modified 17 months ago by lieven.sterck5.5k • written 17 months ago by freddiejung30

What is the scientific/biological question you are looking for an answer to?

Depending on your question there are different initial error correction bfx pipelines that are reccomeded for PacBio data.

ADD REPLYlink modified 17 months ago • written 17 months ago by tjduncan230

Did anyone use FMLRC (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807796) or is HALC better?

ADD REPLYlink written 12 months ago by Ric250
0
gravatar for lieven.sterck
17 months ago by
lieven.sterck5.5k
VIB, Ghent, Belgium
lieven.sterck5.5k wrote:

The build-in error correction procedure of the CANU pipeline works quite well. That is however not using illumina data but only PacBio.

ADD COMMENTlink written 17 months ago by lieven.sterck5.5k
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: 1509 users visited in the last hour