sanger-pathogens / iva
de novo virus assembler of Illumina paired reads
☆55Updated 3 years ago
Alternatives and similar repositories for iva:
Users that are interested in iva are comparing it to the libraries listed below
- ☆52Updated 3 years ago
- Split Kmer Analysis☆63Updated 2 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆70Updated 3 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆44Updated 4 years ago
- IS mapping software☆53Updated 3 years ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆73Updated last year
- a collection of scripts for organising bacterial genomes by species☆76Updated 3 years ago
- Estimate metagenomic coverage and sequence diversity☆48Updated 8 months ago
- A tool for removing redundant genomes from a set of assemblies☆71Updated last year
- ☆36Updated 2 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated last year
- Assembling the cause of phenotypes and genotypes from NGS data☆29Updated 4 years ago
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆58Updated 3 years ago
- Scripts and programs for the Holt Lab's MinION desktop☆32Updated 4 years ago
- ☆81Updated last year
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆47Updated 3 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆57Updated 4 years ago
- A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads☆69Updated 3 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆97Updated 2 weeks ago
- Remove lambda phage reads from a fastq file☆29Updated 2 years ago
- tools for assessing the accuracy of genome assemblies☆34Updated 11 months ago
- Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers☆33Updated last year
- OPAL: Open-community Profiling Assessment tooL☆28Updated 2 months ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆59Updated 5 years ago
- ONT assembly and Illumina polishing pipeline☆91Updated 4 years ago
- SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organism…☆58Updated last year
- Synteny Imager☆61Updated 7 months ago
- Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…☆31Updated last year
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study☆18Updated 4 years ago