proovread error correction (help!)

Question

[midox]

Hello,

I wanted to know is what proovread performs error correction with reference genome (or reference sequence) or de Novo?

because they wrote "the reference sequences"

Thank you for your reply

Answer 1

[Medhat]

proovread:

tool to correct the LR "long read from SMRT" using high quality SR "short reads " generated by illumina sequencer

Primarily proovread has been designed to correct PacBio subreads. You get these reads either from PacBio's SMRT-Portal or by using dextract from Gene Myers PacBio assembler DAZZLER

For correction of long reads, proovread needs high coverage short read data. Typically these are HiSeq (75-150bp) and MiSeq reads (200-300bp)

---

Update:

To use it

/path/to/proovread --long-reads=<FASTA/FASTQ> --short-reads=<FASTA/FASTQ> --threads [default 4]

    -l, --long-reads=<FASTA/FASTQ>
        PacBio subreads or other erroneous sequences to be corrected.

    -s, --short-reads=<FASTA/FASTQ>
        High confidence short reads. Specify mulitple times for multiple
        libs, need to have same format (FASTA/FASTQ and offset 33,64)

          -s lib1.fq -s lib2.fq # use reads from two libs

note;

 [--sam/--bam=<SAM/BAM>]
        External SAM or sorted BAM file instead of --short-reads.

[2]:

[midox]

Thank you for your help.

Yes I know but is that they use a reference genome or reference sequence or not?

[Devon Ryan]

Reread what medhat posted and the paper. There is no reference sequence involved. It uses short reads to correct long reads (i.e., a hybrid approach).