-
Notifications
You must be signed in to change notification settings - Fork 1
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
daccord error correction #3
Comments
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 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 |
thank you for your response. |
Yes, you need DAZZ_DB and DALIGNER. |
the |
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. |
Is it possible to clarify the tuning algorithm? |
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 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. |
No, |
Is there any particular detail you're intersted in? Any particular issues with understanding the paper? |
thank you for your reply. |
any response please? |
the software only for pacbio data ? |
daligner: Block test.2 contains reads < 14bp long ! Run DBsplit |
daccord should work for any kind of data loosely followng it's employed error model of randomly occuring errors. |
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
The text was updated successfully, but these errors were encountered: