SegataLab / cmseq
Set of utilities on sequences and BAM files
☆26Updated 3 years ago
Alternatives and similar repositories for cmseq:
Users that are interested in cmseq are comparing it to the libraries listed below
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆25Updated 2 months ago
- ☆22Updated 4 years ago
- KEGG Module Evaluation Tool☆27Updated last year
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago
- Phasing for metagenomics using PacBio long reads☆17Updated 3 years ago
- MetaSNV, a metagenomic SNV calling pipeline.☆20Updated 2 years ago
- Workflows for metagenomic sequence data processing and analysis.☆17Updated 5 years ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated last year
- Pipeline for metagenome and metatranscriptome joint assembly☆19Updated last year
- Microbial agile accurate SNP Typer☆29Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Prophage Activity Estimator☆26Updated 7 months ago
- HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps☆13Updated last year
- Taxonomic classification of viruses at Order and Family level☆19Updated last year
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆31Updated last year
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated last month
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆44Updated last year
- ☆16Updated 4 years ago
- mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads☆25Updated 2 years ago
- Genomewide Epistasis Analysis on Bacteria☆14Updated 4 months ago
- MAG Circularization Method☆33Updated 2 years ago
- MetaGeneMark-2: Improved Gene Prediction in Metagenomes☆18Updated 9 months ago
- ☆27Updated 2 weeks ago
- This repository contains R code for building a heatmap and histogram with the output of FastANI☆16Updated 3 years ago
- Toolkit for establishing, updating, and validating GTDB species clusters☆20Updated 2 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 9 months ago
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆31Updated 2 years ago
- ☆32Updated last year
- A Shiny app for taxonomic abundance visualization☆7Updated 8 months ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆21Updated last year