awesome_microbiome

The awesome microbiome collects tools, algorithms, workflows, and databases for microbiome.

• tools and databases for amplicon data

• workflows for metagenomes and isolates

• microbial genomes resources

• basecall, qc, correct, polish

• alignment, multi-sequence alignment, sequence cluster

• tool for assembly of short-reads, long-reads, hybrid, and hifi, and polish of assemblies

• binning, strain analysis, and assessment

• genes, elements, and peptides prediction

• metagenome profile based on read, contig, mag and strain

• annotationo tools and databases

• metabolic construction

• comparative genomics

• visualization of alignment/msa, genomes, and assemblies

• build a tree and visualization

• metatranscriptomics

Contribution

Feel free to contribute and submit a PR.

Updates

Star to follow the updates.

Contact

This repository was created by Jie Li.