smdabdoub / kraken-biomLinks
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
☆56Updated 3 years ago
Alternatives and similar repositories for kraken-biom
Users that are interested in kraken-biom are comparing it to the libraries listed below
Sorting:
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆29Updated 5 years ago
- ☆84Updated 2 years ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆59Updated last year
- nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…☆70Updated 3 years ago
- Kraken output generates a report for each datasets, this script takes these individual output and combines it to one file, where each col…☆24Updated last year
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 4 years ago
- Snakemake workflow for metagenomic classification with Kraken2☆66Updated 2 years ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆45Updated 5 years ago
- GTDB taxonomy taxdump files with trackable TaxIds☆55Updated 6 months ago
- Horizontal gene transfer (HGT) identification pipeline☆63Updated 2 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆46Updated 2 years ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆72Updated 5 years ago
- Metagenomics-related extended functionalities to samtools☆22Updated 2 years ago
- FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…☆67Updated 8 months ago
- Scripts and libraries for Environmental Genomics☆38Updated 9 months ago
- Microbiome classification pipeline☆65Updated 6 months ago
- A toolbox for comparative genomics.☆106Updated 4 years ago
- phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.☆88Updated 2 years ago
- An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters☆91Updated last year
- Prediction of prophages from bacterial genomes☆81Updated 5 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆92Updated 3 months ago
- Nextflow pipeline to analyze PacBio HiFi full-length 16S data☆87Updated 4 months ago
- Estimate metagenomic coverage and sequence diversity☆56Updated last year
- Making whole bacterial genome sequencing data analysis easy☆113Updated 6 months ago
- DDBJ Fast Annotation and Submission Tool☆83Updated 2 months ago
- Rapid and scalable correlation estimation for compositional data☆95Updated last year
- IS mapping software☆57Updated 3 years ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆71Updated last year
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study☆18Updated 5 years ago