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 )
☆68Updated 9 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☆69Updated 4 years ago
- GTDB taxonomy taxdump files with trackable TaxIds☆56Updated 8 months ago
- A tool for removing redundant genomes from a set of assemblies☆77Updated 3 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
- Ley Lab MetaGenome Profiler DataBase generator☆50Updated 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
- Microbiome classification pipeline☆65Updated 7 months ago
- Estimate metagenomic coverage and sequence diversity☆58Updated last week
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆62Updated 2 years ago
- Split Kmer Analysis☆66Updated 3 years ago
- IS mapping software☆57Updated 4 years ago
- 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…☆60Updated last year
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆76Updated 2 years ago
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆42Updated 4 years ago
- Perl script for simulating PCR reactions. Extract sequences from a query based on primer sequences.☆48Updated 8 months ago
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆29Updated 5 years ago
- ☆37Updated 3 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆45Updated 5 years ago
- Gene-flank analysis tool☆34Updated last year
- scripts for estimating bacteria replication rates based on population genome copy number variation☆73Updated 6 years ago
- Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.☆27Updated 8 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆61Updated 2 years ago
- Prediction of prophages from bacterial genomes☆81Updated 6 months ago
- Scalable creating/updating of metagenome profiling databases☆63Updated 6 months ago
- Generates an NCBI .tbl file of annotations on a genome.☆68Updated 7 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆54Updated 2 years ago
- A toolkit for prokaryotic comparative genomics☆51Updated 2 months ago
- Sorts amplicons from Nanopore sequencing data based on similarity☆40Updated 2 months ago