Siddarthan Venkatachalam's repositories
Ebame2022_quince_et_al
The tutorials developed by Chris Quince, Rob James and SĂ©bastien Raguideau in EBAME7 2022
ONTrack
A MinION-based pipeline for tracking species biodiversity
pysradb
Package for fetching metadata and downloading data from SRA/ENA/GEO
Kelp_associated_bacterial_genomes
This repository contains code detailing the assembly and analyses of bacterial genomes from bull kelp (Nereocystis luetkeana) blades
BioKIT-1
a versatile toolkit for processing and analyzing diverse types of sequence data
UniteM
Ensemble binning strategies for combining the output of multiple binning methods.
ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn
racon
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
cDNA_Cupcake
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
admixture-wrapper
A tool to automate analyses in admixture, a program used for detecting population structure with SNP data.
dryad-app
Codebase for the collaboration of Dryad and Dash data publication and curation services.
NanoCLUST
NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
metaGEM
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Ocean_tags
Collection of 16S rRNA reads from publicly available ocean metagenomic datasets
r_phylogenetics_worshop
Using ggtree to build phylogenetic trees
phyloFlash
phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
mockcommunity
Long-read mock community experiments
woltka
Web of Life Toolkit App
biokit
Bioinformatics in Python
microeco
An R package for data analysis in microbial community ecology
SqueezeMeta
A complete pipeline for metagenomic analysis
pb-metagenomics-tools
pb-metagenomics-tools
Reactor-metagen
The steps required to repeat bioinformatic analysis used in the manuscript "Microbial dark carbon fixation fueled by nitrate enrichment"