- if you are doing nanopore amplicon sequencing vor SARS-CoV-2 read on, else leave this git :)
- This small parser/tool aims to tell you which minimum set of primer would be need to repair a genome
- the main goal was to learn rust a bit so this git is super basic
# install a gcc compiler if its not available
sudo apt install build-essential
# install rust and go with 1) when prompted
curl https://sh.rustup.rs -sSf | sh
# refresh $PATH or restart terminal
. ~/.profile
git clone https://github.com/replikation/seqrs.git
cd seqrs/
## test run
cargo run -- --genomes data/multifasta_v1200.fasta --primerbed data/Primerfiles/V1200/nCoV-2019.bed --results results.txt
## build and install to path
cargo install --path .
seqrs --genomes data/multifasta_v1200.fasta --primerbed data/Primerfiles/V1200/nCoV-2019.bed --results results.tsv -a 1200
- you get a results.tsv file with the columns
fastaheader forward_primer reverse_primer
seqrs --help
seqrs - sequence repair in rust 0.2.0
Quickly extract primerpairs to amplify missing/masked regions of genomes.
USAGE:
seqrs [OPTIONS] --genomes <genomes> --primerbed <primerbed>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-a, --ampliconsize <ampliconsize> amplicon size [default: 1200]
-g, --genomes <genomes> Fasta file input
-p, --primerbed <primerbed> bed file containing the primer infos
-r, --results <results> tab separated output [default: results.tsv]