bhattlab / StrainSifter
A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
☆19Updated 6 years ago
Alternatives and similar repositories for StrainSifter:
Users that are interested in StrainSifter are comparing it to the libraries listed below
- TAXnomic Profile Aggregation and STAndardisation☆35Updated 3 months ago
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Updated last year
- A repository with scripts to run pipeline that are commonly used in the Meren Lab☆11Updated 7 years ago
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Updated 9 years ago
- OPAL: Open-community Profiling Assessment tooL☆28Updated last month
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…☆24Updated 3 years ago
- MetaSNV, a metagenomic SNV calling pipeline.☆20Updated 2 years ago
- Toolkit for establishing, updating, and validating GTDB species clusters☆20Updated 3 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆40Updated 4 years ago
- Metagenomic species profiling with enhanced coverage of the human gut microbiome☆25Updated 9 months ago
- A Shotgun Metagenome Annotation Pipeline☆23Updated 7 years ago
- Analyze a set of genomes with the anvi'o pangenome pipeline☆17Updated last year
- Phasing for metagenomics using PacBio long reads☆17Updated 3 years ago
- Three bacterial GWAS methods all rolled into one easy-to-use R package☆19Updated 10 months ago
- MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achiev…☆20Updated 3 years ago
- Find Unique genomic Regions☆29Updated last month
- MAG Circularization Method☆33Updated 2 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- Strain Prediction and Analysis with Representative SEquence☆18Updated 2 months ago
- Bacterial genomes finishing tool for structural insights on draft genomes☆24Updated last year
- Strain Resolution ON Graphs☆47Updated last year
- Implementation of Krona to QIIME2☆15Updated 11 months ago
- MetaCompass: Reference-guided Assembly of Metagenomes☆38Updated 4 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Assembling the cause of phenotypes and genotypes from NGS data☆29Updated 4 years 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 3 weeks ago
- mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads☆25Updated 2 years ago
- In-depth characterization and annotation of differences between two sets of DNA sequences☆60Updated 4 years ago