Question: Quake Error Corrector
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gravatar for Seigfried
3.1 years ago by
Seigfried70
Seigfried70 wrote:

Hello I have been trying to run Quake Error Corrector on my Illumina reads before assembly. I am following the manual at http://www.cbcb.umd.edu/software/quake/manual.html. I have a problem running the final step of error correction as Quake always gives an error

"Kmers are not of expected length 21"

As I understand it the Quake program has 3 sub-programs inside it called - 1)Count qmers 2)Coverage Cutoff 3)Correct reads I have tried searching for examples to run Quake but in all of the cases, nobody uses the second program which is Cov_model.py. The Quake.py program is directly run like

quake.py -f pairs.list -k 21

However, there are no commandline options for cut-off value or for providing a count-file.


My commands in brief were-

1) Using jellyfish to get kmer counts.

jellyfish count -m 21 -s 27G -t 48 -C -F 2 File_1.fastq File_2.fastq

This generated a file called mer_counts.jf

2)The second module in jellyfish computes a histogram of k-mer ocurrences.

jellyfish histo -f -t 48 -v -o reads.histo mer_counts.jf

This generated a file called reads.histo containing number of kmers and their multiplicity

3)Then I can plug it into Quake and use

cov_model.py --int reads.histo

This worked well and gave a Coverage Cutoff of 1.

4) I went ahead using reads.histo to the final Correction step

correct -f input_files.txt -k 21 -c 1 -m reads.histo -p 48 -z --log

This just gives me an error saying "Kmers are not of expected length 21"


Should I just go ahead with using Quake.py? It does not provide any options to provide a cutoff file or a count file. Please advise!

quake • 1.4k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Seigfried70
0
gravatar for Seigfried
3.1 years ago by
Seigfried70
Seigfried70 wrote:

Found the problem for anyone interested. Apparently it is a compatibility issue with the new Jellyfish 2.0

Jellyfish 1.1 is compatible with Quake. 2.0 isn't.

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Seigfried70
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