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daccord error correction #3

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Mkchouk opened this issue Jun 13, 2017 · 14 comments
Open

daccord error correction #3

Mkchouk opened this issue Jun 13, 2017 · 14 comments

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@Mkchouk
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Mkchouk commented Jun 13, 2017

Hello,
can you present us how we correct long reads using daccord?
i must just run ./src/daccord reads.las reads.dam ?
and how generete reads.las and reads.dam ?

thanks

@gt1
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gt1 commented Jun 13, 2017

As the README.md says, you need to first convert your input FastA file(s) to a dazzler database using fasta2DB or fasta2DAM from DAZZ_DB . Use something like

fasta2DAM reads.dam reads.fasta
DBsplit -s256 -x1000 reads.dam

Then run daligner on this database to produce alignments in the LAS format. Try

HPC.daligner reads.dam | bash

You need to have the daligner directory in your PATH for this to work.

Afterwards you can run

src/daccord reads.las reads.dam >reads_daccord.fasta

@Mkchouk
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Mkchouk commented Jun 13, 2017

thank you for your response.
so i must install Dazzler databases and DALIGNER for LAS alignment files??
thank you

@gt1
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gt1 commented Jun 13, 2017

Yes, you need DAZZ_DB and DALIGNER.

@Mkchouk
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Mkchouk commented Jun 13, 2017

the HPC.daligner reads.dam | bash generated me three .las files.
i run daccord for every file to obtain the corrected reads?
src/daccord reads.1.las reads.dam >reads_daccord.1.fasta
src/daccord reads.2.las reads.dam >reads_daccord.2.fasta
src/daccord reads.3.las reads.dam >reads_daccord.3.fasta
thank you for your response

@gt1
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gt1 commented Jun 14, 2017

Yes. Each of the LAS files contains alignments for a block of reads. daccord will output corrected reads for the reads it finds in these files.

@Mkchouk
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Mkchouk commented Jun 14, 2017

Is it possible to clarify the tuning algorithm?
There are many mathematical equations and since I am not a mathematician I have a hard time understanding the algorithm generally.
thank you

@gt1
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gt1 commented Jun 15, 2017

The program should be just fine with it's default settings. If you are looking at a repetitive genome, you may consider setting the -D parameter to twice the average sequencing depth, i.e. use -D60 for a sequencing depth of 30. This will only load the (up to) 60 "best" alignments for each read. You may also consider to run

computeintrinsicqv -d30 reads.db reads.las
lasfilteralignments reads.db reads.las

which will create reads_filtered.las . Here the -d switch needs to be set to the average sequencing depth. Afterwards pass reads_filtered.las to daccord.

@Mkchouk
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Mkchouk commented Jul 3, 2017

No,
It's not my question.
My question is to clarify the daccord algorithm,
How does daccord do the long reads error correction?
thanks

@gt1
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gt1 commented Jul 11, 2017

Is there any particular detail you're intersted in? Any particular issues with understanding the paper?

@Mkchouk
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Mkchouk commented Jul 11, 2017

thank you for your reply.
Yes. I did not understand how daccord correct long reads.
I want to understand the daccord algorithm.
Can you detail the algorithm please?
thank you

@Mkchouk
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Mkchouk commented Jul 24, 2017

any response please?
Thanks

@smm19900210
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the software only for pacbio data ?

@smm19900210
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daligner: Block test.2 contains reads < 14bp long ! Run DBsplit
what's wrong?

@gt1
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gt1 commented Aug 30, 2018

daccord should work for any kind of data loosely followng it's employed error model of randomly occuring errors.

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