thomasgurry / amplicon_sequencing_pipelineLinks
Pipeline for computing OTU tables from 16S or ITS amplicon sequencing data.
☆32Updated 2 years ago
Alternatives and similar repositories for amplicon_sequencing_pipeline
Users that are interested in amplicon_sequencing_pipeline are comparing it to the libraries listed below
Sorting:
- Snakemake workflow for metagenomic classification with Kraken2☆66Updated 2 years ago
- ☆32Updated 2 years ago
- mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads☆25Updated 2 years ago
- Analysing Metagenomic Species (MGS)☆42Updated 5 years ago
- ☆23Updated 7 years ago
- Computational workflows for metagenomics tasks, by the Bhatt lab☆47Updated 2 years ago
- Statistical analysis for sparse high-throughput sequencing☆70Updated 11 months ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆56Updated 3 years ago
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆58Updated 4 years ago
- Rank-based Gene Ontology analysis of gene expression data☆42Updated 2 years ago
- Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers☆34Updated last year
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆59Updated last year
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber☆66Updated last year
- This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical…☆42Updated 6 years ago
- Metagenomics Workshop☆28Updated 8 years ago
- HoCoRT - Remove specific organisms from sequencing reads☆17Updated 10 months ago
- A repository for the lessons and notebooks used for Binder tutorials☆14Updated 5 years ago
- Protein Alignment and Detection Interface☆60Updated last year
- MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.☆16Updated 2 years ago
- catalog for long-read sequencing tools☆32Updated 2 years ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆33Updated 5 years ago
- VAPiD: Viral Annotation and Identification Pipeline☆54Updated last year
- ☆40Updated 4 years ago
- gutSMASH☆56Updated last month
- A microbial profiling framework for metagenomic analysis☆24Updated 5 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
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 4 years ago
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆53Updated 5 months ago
- A general metagenomics data mining system focus on robust microbiome research☆58Updated last year
- Get, parse, and extract information from the SRA metadata files☆45Updated 3 years ago