hsgweon / pipitsLinks
Automated pipeline for analyses of fungal ITS from the Illumina
☆32Updated 7 months ago
Alternatives and similar repositories for pipits
Users that are interested in pipits are comparing it to the libraries listed below
Sorting:
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆72Updated 2 years ago
- ☆23Updated 7 years ago
- A set of R scripts for the analysis of microbial profiles☆41Updated last year
- 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
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆39Updated 2 years ago
- SHallow shOtGUN profiler☆53Updated 3 years ago
- A robust and fast clustering method for amplicon-based studies☆31Updated 2 years ago
- The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…☆72Updated 3 years ago
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆77Updated 5 months ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆33Updated 5 years ago
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆106Updated 10 months ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆47Updated 5 years ago
- Phylogenetic and taxonomic analysis for genomes and metagenomes☆82Updated 9 years ago
- Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake☆50Updated last year
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆61Updated 2 years ago
- Compare different differential abundance and expression methods☆52Updated 3 years ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 8 years ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆93Updated 3 weeks ago
- Speedy versions of phyloseq functions☆48Updated last year
- BEAV: Bacterial Element Annotation reVamped☆72Updated 4 months ago
- ☆79Updated 2 years ago
- GraftM - Rapid community profiles from metagenomes☆47Updated last month
- scripts for estimating bacteria replication rates based on population genome copy number variation☆73Updated 6 years ago
- Scripts and tutorials on how to assemble individual microbial genomes from metagenomes☆80Updated 9 years ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆60Updated last year
- Genome wide orthology inference and dNdS estimation☆96Updated 3 months ago
- Micro 612 genomics workshop☆38Updated 4 years ago
- PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes☆32Updated 4 months ago
- Sparse Cooccurence Network Investigation for Compositional data☆25Updated last year
- Massively parallel phylogenetic placement of genetic sequences☆86Updated 3 years ago