arumugamlab / msamtools
Metagenomics-related extended functionalities to samtools
☆20Updated last year
Alternatives and similar repositories for msamtools:
Users that are interested in msamtools are comparing it to the libraries listed below
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆54Updated this week
- ☆65Updated 2 months ago
- GTDB taxonomy taxdump files with trackable TaxIds☆52Updated 10 months ago
- Improvement of metagenome-assembled genomes☆50Updated 4 years ago
- ☆49Updated 10 months ago
- MaAsLin3: Microbiome Multivariate Association with Linear Models☆29Updated this week
- AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resis…☆32Updated 3 months ago
- MetaGeneMark-2: Improved Gene Prediction in Metagenomes☆18Updated 11 months ago
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆54Updated last month
- ☆28Updated last year
- BEAV: Bacterial Element Annotation reVamped☆61Updated 4 months ago
- Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data☆14Updated this week
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated last week
- EzAAI - High Throughput Prokaryotic AAI Calculator☆38Updated 4 months ago
- CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data☆22Updated this week
- Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …☆32Updated 4 years ago
- ☆45Updated last year
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated last year
- Discover and annotate the virome☆37Updated 4 months ago
- A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations☆40Updated last year
- Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project☆11Updated 2 years ago
- A toolkit for prokaryotic comparative genomics☆45Updated last month
- scripts for estimating bacteria replication rates based on population genome copy number variation☆70Updated 5 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more☆27Updated last year
- Tool to estimate genome quality of microbial eukaryotes☆36Updated last month
- Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.☆23Updated 4 months ago
- A pipeline to computationally identify invertible DNA regions and quantify their orientations.☆29Updated last year
- A microbiome analysis toolkit for R☆22Updated last year
- Ley Lab MetaGenome Profiler DataBase generator☆49Updated 2 years ago