This software is now deprecated, see this blog post for details
A prototype nanopore correction pipeline. It self-error-corrects OxfordNanopore data.
These must all be on your $PATH.
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.