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.

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