HRGV / phyloFlash
phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
☆77Updated last year
Related projects ⓘ
Alternatives and complementary repositories for phyloFlash
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆108Updated 6 months ago
- A toolbox for pangenome analysis and threshold evaluation.☆91Updated 2 years ago
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆110Updated last year
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆108Updated last week
- A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework☆78Updated 5 months ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆56Updated 7 months ago
- A toolbox for comparative genomics.☆97Updated 3 years ago
- Supporting code for uncultivated gut virus manuscript☆66Updated last year
- Pairwise SNP distance matrix from a FASTA sequence alignment☆127Updated 8 months ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆71Updated 3 months ago
- Collection of scripts for bacterial genomics☆44Updated 4 years ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆63Updated 11 months ago
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆27Updated 4 years ago
- CLI tool to annotate genes with KOfam☆72Updated last year
- Massively parallel phylogenetic placement of genetic sequences☆78Updated 2 years ago
- Making whole bacterial genome sequencing data analysis easy☆99Updated 2 weeks ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆71Updated 11 months ago
- A hybrid assembly and MAG recovery pipeline (and more!)☆85Updated this week
- a collection of scripts for organising bacterial genomes by species☆76Updated 2 years ago
- Foreign Contamination Screening caller scripts and documentation☆107Updated this week
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆70Updated last year
- MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data☆92Updated 7 months ago
- This is the source code for multisamples ARGs profiling using SARG2.0 database☆45Updated 3 years ago
- SKESA assembler☆112Updated last month
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study☆18Updated 4 years ago
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆110Updated last week
- Detection of pseudogene candidates in bacterial and archaeal genomes.☆45Updated 8 months ago
- Metagenomic classification of long-read sequencing data☆62Updated this week
- ☆79Updated last year
- A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concat…☆53Updated 3 months ago