bhattlab / StrainSifterLinks
A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
☆19Updated 7 years ago
Alternatives and similar repositories for StrainSifter
Users that are interested in StrainSifter are comparing it to the libraries listed below
Sorting:
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆39Updated last year
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Updated 2 years ago
- OPAL: Open-community Profiling Assessment tooL☆29Updated 10 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Output FASTQ summary statistics in JSON format☆29Updated 3 years ago
- A Shotgun Metagenome Annotation Pipeline☆23Updated 8 years ago
- FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…☆24Updated 4 years ago
- MetaSNV, a metagenomic SNV calling pipeline.☆20Updated 3 years ago
- Identify phenotype-specific k-mers and predict phenotype using sequenced bacterial strains☆20Updated last week
- Toolkit for establishing, updating, and validating GTDB species clusters☆20Updated last month
- Bioinformatics pipeline for nanopore sequencing data☆11Updated 6 years ago
- CAMITAX: Taxon labels for microbial genomes☆30Updated last year
- Highly sensitive pathogen detection☆12Updated 5 years ago
- A method of assessing sequence complexity based on kmer frequencies☆33Updated 7 years ago
- A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…☆19Updated last year
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Updated 2 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 6 years ago
- Strain Resolution ON Graphs☆48Updated 2 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆43Updated 5 years ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆31Updated last year
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Updated 9 years ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Updated 2 years ago
- ANNOgesic - A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes☆32Updated last year
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated 2 years ago
- A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies☆32Updated 2 years ago
- In-depth characterization and annotation of differences between two sets of DNA sequences☆63Updated 5 years ago
- A repository with scripts to run pipeline that are commonly used in the Meren Lab☆11Updated 7 years ago
- A containerized bioinformatics pipeline for viral metagenomic data analysis☆37Updated last year
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- Influenza genome analysis Nextflow workflow☆24Updated 2 months ago