Finn-Lab / MAG_Snakemake_wf
Recovery of prokaryotic genomes from shotgun metagenomic sequencing data
☆57Updated 3 years ago
Alternatives and similar repositories for MAG_Snakemake_wf:
Users that are interested in MAG_Snakemake_wf are comparing it to the libraries listed below
- ☆49Updated 4 years ago
- Contains a fasta format database of a large variety of mobile genetic elements and an annotation file☆44Updated 3 years ago
- Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more☆27Updated last year
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆28Updated 5 years ago
- A wrapper to identify, bin, classify, and predict host-viral relationship for viruses☆70Updated last month
- ☆48Updated 10 months ago
- Horizontal gene transfer (HGT) identification pipeline☆56Updated last year
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- This is the source code for multisamples ARGs profiling using SARG2.0 database☆46Updated 3 years ago
- A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during…☆64Updated 6 months ago
- GTDB taxonomy taxdump files with trackable TaxIds☆52Updated 9 months ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆52Updated 2 years ago
- ☆79Updated last year
- MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.☆88Updated 6 months ago
- Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets☆69Updated 7 months ago
- ☆28Updated last year
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆71Updated last year
- ☆50Updated 11 months ago
- Nextflow pipeline to analyze PacBio HiFi full-length 16S data☆66Updated this week
- Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and …☆31Updated last year
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆42Updated last year
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆115Updated last year
- ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Dat…☆52Updated 11 months ago
- A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category☆60Updated 5 months ago
- Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biot…☆62Updated 4 years ago
- code repo for mobileOG-db☆34Updated 3 weeks ago
- Metatranscriptomics Tutorial☆60Updated last year
- Detection of pseudogene candidates in bacterial and archaeal genomes.☆46Updated 10 months ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆70Updated 5 years ago
- Classifiers trained on commonly used variable regions of Prokaryotic 16S rRNA genes☆13Updated 7 months ago