Siddarthan Venkatachalam's repositories
A-microbiologist-wants-to-compute
This repo collects the list of learning online resources related to microbiome computational science and tools.
BiG-SCAPE
Similarity networks of biosynthetic gene clusters
Ebame2022_quince_et_al
The tutorials developed by Chris Quince, Rob James and SĂ©bastien Raguideau in EBAME7 2022
FalkorMetaT
Bioinformatic pipeline and data processing steps used to analyze eukaryotic metatranscriptomes
Filtlong
quality filtering tool for long reads
FRAM_EGC_2016_2020_data_analysis
Data files and analysis pipelines for amplicon and metagenomic data generated from autonomously collected water samples in the East Greenland Current (Fram Strait) between 2016 - 2020
hifiasm-meta
hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
homopolish
High-quality Nanopore-only genome polisher
HyLight
HyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NGS and 3rd generation sequencing to rapidly and accurately assemble highly complex metagenomic sequencing data.
laca
A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)
metaMDBG
MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
MetONTIIME
A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework
Microbiome-conferences-c
This repo collects the list of conferences/meetings/workshops etc. related to microbiome science and tools.
Microbiome-etc-Podcasts
This repo collects the list of podcasts related to microbiome science.
NanoPhase
Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and short reads (hybrid strategy)
NanoR
Nanopore data analysis in R
NanoRTax
Real-time analysis pipeline for nanopore 16S rRNA data
NextDenovo
Fast and accurate de novo assembler for long reads
ONTrapid
ONT assembly pipeline
pepper
PEPPER-Margin-DeepVariant
proovframe
frame-shift correction for long-read (meta)genomics
SAOB_Metaproteogenomics
Metabolic networks of a syntrophic-acetate oxidizing lab-scale bioreactor community
shasta
De novo assembly from Oxford Nanopore reads.
SprayNPray
Rapid and simple taxonomic profiling of genome and metagenome contigs
stRainy
Graph-based assembly phasing
strainyMAG
ONT pipeline
Trycycler
A tool for generating consensus long-read assemblies for bacterial genomes
wtdbg2
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly