artic-network / artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
☆168Updated last year
Alternatives and similar repositories for artic-ncov2019:
Users that are interested in artic-ncov2019 are comparing it to the libraries listed below
- snipit: summarise snps relative to your reference sequence☆151Updated this week
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Updated last year
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆119Updated 2 weeks ago
- The ARTIC field bioinformatics pipeline☆119Updated last week
- Scan contig files against PubMLST typing schemes☆210Updated 2 years ago
- "Reads to report" for public health and clinical microbiology☆137Updated 10 months ago
- Finds SNP sites from a multi-FASTA alignment file☆248Updated 4 years ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆314Updated 8 months ago
- ☆197Updated last week
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆216Updated last year
- Assembly and intrahost/low-frequency variant calling for viral samples☆129Updated this week
- Pairwise SNP distance matrix from a FASTA sequence alignment☆128Updated 10 months ago
- RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag☆172Updated 3 years ago
- Generate an interactive dot plot from mummer or minimap alignments☆195Updated last year
- Tool to plot synteny and structural rearrangements between genomes☆294Updated 2 months ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆134Updated 3 months ago
- BSR-Based Allele Calling Algorithm☆139Updated last week
- Processing pipeline for pan-genome visulization and exploration☆137Updated last year
- Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads☆106Updated last year
- Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data☆133Updated 3 years ago
- Bacterial ribosomal RNA predictor☆232Updated last year
- Convert various sequence formats to FASTA☆127Updated 2 years ago
- Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model☆161Updated 2 years ago
- Quality control for MinION sequencing data☆215Updated 2 years ago
- Benchmarking of long-read assembly tools for bacterial whole genomes☆170Updated 3 years ago
- (Not Offical) BBMap short read aligner, and other bioinformatic tools.☆216Updated 3 years ago
- Fast and accurately polish the genome generated by long reads.☆217Updated 3 weeks ago
- RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.☆240Updated 2 months ago
- NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…☆295Updated 10 months ago
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆183Updated 8 months ago