lmrodriguezr / enveomicsLinks
Scripts and libraries for Environmental Genomics
☆38Updated 4 months ago
Alternatives and similar repositories for enveomics
Users that are interested in enveomics are comparing it to the libraries listed below
Sorting:
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆55Updated 3 years ago
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆59Updated 5 years ago
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study☆18Updated 5 years ago
- ☆82Updated last year
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆74Updated 2 years ago
- IS mapping software☆54Updated 3 years ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆72Updated 5 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆70Updated 3 years ago
- DDBJ Fast Annotation and Submission Tool☆79Updated last month
- Snakemake workflow for metagenomic classification with Kraken2☆65Updated 2 years ago
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆30Updated 5 years ago
- Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets☆71Updated last year
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- Ley Lab MetaGenome Profiler DataBase generator☆50Updated 2 years ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆56Updated last year
- Horizontal gene transfer (HGT) identification pipeline☆59Updated 2 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- GTDB taxonomy taxdump files with trackable TaxIds☆54Updated last month
- MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.☆88Updated 10 months ago
- A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category☆67Updated last month
- A tool for removing redundant genomes from a set of assemblies☆71Updated last year
- ☆72Updated last month
- Perl script for simulating PCR reactions. Extract sequences from a query based on primer sequences.☆47Updated 2 months ago
- ☆52Updated last year
- Reorients assembled microbial sequences☆121Updated 3 months ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆59Updated last week
- a collection of scripts for organising bacterial genomes by species☆76Updated 3 years ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆58Updated last year
- Kraken output generates a report for each datasets, this script takes these individual output and combines it to one file, where each col…☆23Updated 11 months ago
- Microbiome classification pipeline☆66Updated last month