transcript / samsa2Links
SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
☆61Updated last year
Alternatives and similar repositories for samsa2
Users that are interested in samsa2 are comparing it to the libraries listed below
Sorting:
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆68Updated 4 years ago
- Snakemake workflow for metagenomic classification with Kraken2☆67Updated 2 years ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆57Updated 3 years ago
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆81Updated 2 years ago
- Bioinformatics Tools☆90Updated 2 weeks ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆46Updated 2 years ago
- ☆84Updated 2 years ago
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆29Updated 6 years ago
- IS mapping software☆57Updated 4 years ago
- Development version of Easyfig☆104Updated 2 years ago
- MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.☆89Updated last year
- Making whole bacterial genome sequencing data analysis easy☆113Updated 9 months ago
- DDBJ Fast Annotation and Submission Tool☆84Updated 4 months ago
- Metatranscriptomics Tutorial☆66Updated 2 years ago
- A scalable bacterial genome assembly, annotation and analysis pipeline☆74Updated 2 years ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆73Updated 6 years ago
- Collection of scripts for bacterial genomics☆48Updated 6 years ago
- nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…☆72Updated 3 years ago
- FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…☆67Updated 10 months ago
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆124Updated last week
- A toolbox for comparative genomics.☆108Updated 4 years ago
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆65Updated 6 years ago
- Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets☆75Updated last year
- Convert GTDB taxonomy to NCBI taxdump format☆74Updated 2 years ago
- Prediction of prophages from bacterial genomes☆81Updated this week
- GraftM - Rapid community profiles from metagenomes☆48Updated 3 months ago
- Recovery of prokaryotic genomes from shotgun metagenomic sequencing data☆62Updated 4 years ago
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study☆17Updated 5 years ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆120Updated last year
- Horizontal gene transfer (HGT) identification pipeline☆67Updated 2 years ago