Experimental pipeline for correcting nanopore reads
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README.md

This software is now deprecated, see this blog post for details

A prototype nanopore correction pipeline. It self-error-corrects OxfordNanopore data.

Dependencies:

These must all be on your $PATH.

Example:

First, build the DALIGNER database and compute alignments:

./nanocorrect-overlap INPUT=reads.fasta NAME=nc

INPUT is the path to your reads. The NAME variable is the prefix you want to use for the output files.

You can correct a range of reads using the python script:

python nanocorrect.py nc 1000:1020 > corrected.fasta

You can correct all reads using the python script:

python nanocorrect.py nc all > corrected.fasta

The first argument must be the same as the NAME variable above. The second is the indices of the reads (in the original fasta) that you want to correct.