SegataLab / cmseq
Set of utilities on sequences and BAM files
☆27Updated 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…☆27Updated 2 months ago
- Trans-Kingdom Marker Gene Pipeline for Taxonomic Profiling of Human Metagenomes☆19Updated last year
- Phasing for metagenomics using PacBio long reads☆17Updated 3 years ago
- ☆22Updated 5 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆31Updated 2 years ago
- Pipeline for metagenome and metatranscriptome joint assembly☆21Updated 2 years ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated 2 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆33Updated last month
- KEGG Module Evaluation Tool☆29Updated last year
- HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps☆14Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- Prophage Activity Estimator☆26Updated 10 months ago
- Bacterial GWAS analysis☆39Updated this week
- HoCoRT - Remove specific organisms from sequencing reads☆17Updated 3 months ago
- This repository contains R code for building a heatmap and histogram with the output of FastANI☆16Updated 3 years ago
- ☆15Updated last year
- 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 2 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago
- ☆24Updated 6 years ago
- MetaSNV, a metagenomic SNV calling pipeline.☆20Updated 3 years ago
- MAG Circularization Method☆33Updated 2 years ago
- ☆16Updated 4 years ago
- Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data☆14Updated last month
- ☆18Updated 3 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- MetaGeneMark-2: Improved Gene Prediction in Metagenomes☆21Updated last year
- ☆32Updated last year
- mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads☆25Updated 2 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 6 years ago