This repository contains two scripts assisting working on nanopore
sequenced amplicons. First is polish_amplicon.sh which takes fasta
file of nanopore reads, clusters them according to similarity,
corrects by multiple alignment and maps the alignment consesuses to
reference genome.
This protocol is heavily influenced by nanocorrect
usage:
./polish_amplicon.sh [-c WORKDIR] [-r REF.fasta] input.fasta
-c WORKDIR Continue work on this directory
-r REF.fasta Genome reference for mapping the final results.
-h Show this message and exit.
Another script is used for separating amplicon reads that are almost equal and are separated by discovery of short "splitter" reads.
usage:
./split_reads.sh -F splitters.fasta sequence.(fast5|fasta)
Map short sequences in splitters.fasta to reads in sequence.fasta and
generate SAM like output file usable for e.g. split_fasta_by_sam.py
-F splitters.fast(a|5) Split the reads according to alignment to these.
-d Use default lastal arguments, instead of ones for nanopore reads
-h Show this message and exit.
These scripts have dependency on sumaclust and poaV2. These need to be in $PATH.
If you use this software in academic publications, please cite
“Detection and Analysis of Somatic LINE-1 Insertions in Colorectal Cancer by Long-distance Inverse-PCR and Nanopore Sequencing” by Pradhan et al. (Submitted)