GlobalPneumoSeq / gps-pipelineLinks
Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project)
☆20Updated last month
Alternatives and similar repositories for gps-pipeline
Users that are interested in gps-pipeline are comparing it to the libraries listed below
Sorting:
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆64Updated 5 months ago
- post processing of bacterial pangenome gene presence/absence matrices☆63Updated 9 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆32Updated last week
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Updated 4 years ago
- Recombination-free trees☆62Updated 3 months ago
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆76Updated 2 years ago
- A tool for removing redundant genomes from a set of assemblies☆77Updated 3 months ago
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆55Updated last month
- MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG stand…☆15Updated last year
- Predict plasmids from uncorrected long read data☆41Updated last month
- plasmidVerify: plasmid contig verification tool☆15Updated 5 years ago
- Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at …☆13Updated 3 years ago
- Gene Absence Presence Identification tool.☆27Updated 8 months ago
- Small utility script to submit genomes to PHASTER for phage detection☆24Updated 4 years ago
- Lightweight bioinformatics pipeline for microbial genome recovery☆18Updated last month
- Bacterial GWAS analysis☆46Updated last month
- Identify phage regions in bacterial genomes for masking purposes☆34Updated 6 years ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆32Updated 7 months ago
- Order and orientation of complete bacterial genomes☆29Updated 5 months ago
- ☆20Updated last year
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆81Updated this week
- a collection of scripts for organising bacterial genomes by species☆81Updated 3 years ago
- Plasmid exploration of bacterial genomes☆22Updated 3 years ago
- Calculate assocations between genes and traits☆29Updated 9 months ago
- Split Kmer Analysis☆65Updated 3 years ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆21Updated 2 years ago
- IslandPath standalone software☆34Updated 2 years ago
- Code Safety Inspection Service☆20Updated 3 years ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆44Updated 4 months ago