Redundans options for the pipeline with all the steps

[alexis groppi]

Hi,

I will use your Redundans pipeline on a draft assembly of big genome (500 Mb) from pacbio reads with canu 1.4. (~100X)
in the examples from the README there is :

# reduction, reference-based scaffolding and gap closing with paired-end reads
./redundans.py -v -i test/600_?.fq.gz -r test/ref.fa -f test/contigs.fa -o test/run_ref_pe-closing --noscaffolding

In this case for the pipeline with all the steps (reduction, scaffolding and gap-filling), the --noscaffolding option shoudn't be there ?
Am I right ?

Thanks for your help

Best regards

Alexis

[l.p.p...@gmail.com]

Hi Alexis, 

No, just run redundans with long reads:

./redundans.py -v -l pacbio_reads.fq.gz -f contigs.fa -o redundans_out

You can add -r reference.fa if there is some closely-related genome sequenced. But it's not necessary. 

Note, the support for long reads is experimental, meaning it should work in most cases, but it's not extensively tested yet... 

Let me know how it worked! 

Hope it helps, 

L. 

L.

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[alexis groppi]

Hi Leszek,

Thanks for your answer.
I have also Illumina reads produced on the same genome (about 16X ; is this sufficient ?)
In your opinion, would it be better to use them instead of the PacBio reads ?

Thanks again

Best regards

Alexis

Le lundi 27 février 2017 14:08:09 UTC+1, lpryszcz a écrit :

Hi Alexis, 

No, just run redundans with long reads:

./redundans.py -v -l pacbio_reads.fq.gz -f contigs.fa -o redundans_out

You can add -r reference.fa if there is some closely-related genome sequenced. But it's not necessary. 

Note, the support for long reads is experimental, meaning it should work in most cases, but it's not extensively tested yet... 

Let me know how it worked! 

Hope it helps, 

L. 

L.

2017-02-27 11:44 GMT+01:00 alexis groppi <agr...@gmail.com>:

Hi,

I will use your Redundans pipeline on a draft assembly of big genome (500 Mb) from pacbio reads with canu 1.4. (~100X)
in the examples from the README there is :

# reduction, reference-based scaffolding and gap closing with paired-end reads
./redundans.py -v -i test/600_?.fq.gz -r test/ref.fa -f test/contigs.fa -o test/run_ref_pe-closing --noscaffolding

In this case for the pipeline with all the steps (reduction, scaffolding and gap-filling), the --noscaffolding option shoudn't be there ?
Am I right ?

Thanks for your help

Best regards

Alexis

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