FOI-Bioinformatics / flextaxdLinks
FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
☆67Updated 10 months ago
Alternatives and similar repositories for flextaxd
Users that are interested in flextaxd are comparing it to the libraries listed below
Sorting:
- ☆84Updated 2 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆68Updated 4 years ago
- IS mapping software☆57Updated 4 years ago
- A tool for removing redundant genomes from a set of assemblies☆78Updated 5 months ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆46Updated 2 years ago
- Microbiome classification pipeline☆65Updated 8 months ago
- GTDB taxonomy taxdump files with trackable TaxIds☆57Updated 9 months ago
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆80Updated 2 years ago
- Prediction of prophages from bacterial genomes☆81Updated last week
- Ley Lab MetaGenome Profiler DataBase generator☆49Updated 3 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
- Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.☆28Updated 9 months ago
- Estimate metagenomic coverage and sequence diversity☆59Updated last month
- a collection of scripts for organising bacterial genomes by species☆81Updated 3 years ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆61Updated last year
- scripts for estimating bacteria replication rates based on population genome copy number variation☆73Updated 6 years ago
- Bioinformatics tool to find integrons in bacterial genomes☆83Updated 9 months ago
- Split Kmer Analysis☆67Updated 3 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Updated 5 years ago
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆29Updated 6 years ago
- A toolkit for prokaryotic comparative genomics☆51Updated 3 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆61Updated 2 years ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆48Updated 5 years ago
- whole genome MLST analysis☆51Updated 7 months ago
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆54Updated 3 months ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- tools for assessing the accuracy of genome assemblies☆35Updated last year
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆43Updated 4 years ago
- Horizontal gene transfer (HGT) identification pipeline☆67Updated 2 years ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆63Updated 2 years ago