replikation / seqrs

sequence tools via rust

SEQuence Repair via ruSt

• 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

Installation from source

1. install rust (if you dont have it)

# 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

2. install seqrs

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 .

run

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

help

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]