bhattlab / StrainSifter
A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
☆19Updated 6 years ago
Related projects ⓘ
Alternatives and complementary repositories for StrainSifter
- A repository with scripts to run pipeline that are commonly used in the Meren Lab☆11Updated 6 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated last year
- TAXnomic Profile Aggregation and STAndardisation☆34Updated 3 weeks ago
- MetaSNV, a metagenomic SNV calling pipeline.☆20Updated 2 years ago
- Toolkit for establishing, updating, and validating GTDB species clusters☆20Updated this week
- Analyze a set of genomes with the anvi'o pangenome pipeline☆17Updated last year
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Updated last year
- OPAL: Open-community Profiling Assessment tooL☆27Updated 3 months ago
- MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achiev…☆19Updated 3 years ago
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆19Updated 8 years ago
- A containerized bioinformatics pipeline for viral metagenomic data analysis☆25Updated 3 months ago
- MAG Circularization Method☆33Updated 2 years ago
- Set of utilities on sequences and BAM files☆25Updated 3 years ago
- shotgun pipeline☆11Updated 5 years ago
- A Shotgun Metagenome Annotation Pipeline☆23Updated 7 years ago
- A shiny package for microbiome functional enrichment analysis☆36Updated 3 weeks ago
- Assembling the cause of phenotypes and genotypes from NGS data☆29Updated 4 years ago
- Implementation of Krona to QIIME2☆14Updated 8 months ago
- Strain Resolution ON Graphs☆47Updated last year
- A repository for the lessons and notebooks used for Binder tutorials☆13Updated 4 years ago
- Find Unique genomic Regions☆29Updated this week
- FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…☆23Updated 3 years ago
- A method of assessing sequence complexity based on kmer frequencies☆28Updated 6 years ago
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆36Updated 2 months ago
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- Three bacterial GWAS methods all rolled into one easy-to-use R package☆19Updated 7 months ago
- ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then sear…☆28Updated 7 months ago
- Strain Prediction and Analysis with Representative SEquence☆18Updated 2 weeks ago
- ☆23Updated 5 years ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated last year