Tools and utilities for running Dockerized metagenomics tools in the Cloud
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Updated
Apr 8, 2019 - C++
Tools and utilities for running Dockerized metagenomics tools in the Cloud
MetaCache-MPI is a software tool that allows to use the metagenomics minhashing algorithm from metacache by means of a High Performance Computing environment by using the MPI library.
genome sized sequences clustering
Fast in-silico normalization algorithm for NGS data
Code for systematically classify data in SRA according to all the taxa present in the reads (SRA-metagenome)
Estimate metagenomic coverage and sequence diversity
QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture
Fast and accurate genomic distances using HyperLogLog
fast classification of metagenomic sequences with lightweight de Bruijin graph-based reference indexing
mGEMS Genomic epidemiology with mixed samples
KOMB is a tool for fast identification of unitigs of interest in metagenomes. KOMB introduces the concept of a Hybrid Unitig Graph (an extension to compacted de Bruijn graphs) and relies on k-core and K-truss decomposition algorithms.
LAMBDA – the Local Aligner for Massive Biological DatA
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Fast and space-efficient taxonomic classification of long reads
Accurate taxonomic classification and abundance profiling using locality-sensitive hashing.
Bonsai: Fast, flexible taxonomic analysis and classification
Ultra-fast and memory-efficient (meta-)genome assembler
Fast sequence vectorization for metagenomics analysis. Converts input sequences into k-mer coverage vectors, fast! Read more detail in our paperhttps://doi.org/10.1093/bioinformatics/btaa441
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