srisvs33

A-microbiologist-wants-to-compute

This repo collects the list of learning online resources related to microbiome computational science and tools.

admixture-wrapper

A tool to automate analyses in admixture, a program used for detecting population structure with SNP data.

AMRocks

Scripts used for Atlantis Massif crustal and sediment microbial analysis

ANI

Calculate Average Nucleotide Identity (ANI) for prokaryotic genomes

ANIclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn

atlas

ATLAS - Three commands to start analyzing your metagenome data

automatic_MAG_refinement

BiG-SCAPE

Similarity networks of biosynthetic gene clusters

biokit

Bioinformatics in Python

BioKIT-1

a versatile toolkit for processing and analyzing diverse types of sequence data

srisvs33/A-microbiologist-wants-to-compute

This repo collects the list of learning online resources related to microbiome computational science and tools.

srisvs33/BiG-SCAPE

Similarity networks of biosynthetic gene clusters

srisvs33/COMEBin

srisvs33/Ebame2022_quince_et_al

The tutorials developed by Chris Quince, Rob James and Sébastien Raguideau in EBAME7 2022

srisvs33/FalkorMetaT

Bioinformatic pipeline and data processing steps used to analyze eukaryotic metatranscriptomes

srisvs33/Filtlong

quality filtering tool for long reads

srisvs33/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

srisvs33/GraphMB

srisvs33/hifiasm-meta

hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.

srisvs33/homopolish

High-quality Nanopore-only genome polisher

srisvs33/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.

srisvs33/laca

A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)

srisvs33/metaMDBG

MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.

srisvs33/MetONTIIME

A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework

srisvs33/Microbiome-conferences-c

This repo collects the list of conferences/meetings/workshops etc. related to microbiome science and tools.

srisvs33/Microbiome-etc-Podcasts

This repo collects the list of podcasts related to microbiome science.

srisvs33/NanoPhase

Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and short reads (hybrid strategy)

srisvs33/NanoR

Nanopore data analysis in R

srisvs33/NanoRTax

Real-time analysis pipeline for nanopore 16S rRNA data

srisvs33/NextDenovo

Fast and accurate de novo assembler for long reads

srisvs33/ONTrapid

ONT assembly pipeline

srisvs33/pepper

PEPPER-Margin-DeepVariant

srisvs33/proovframe

frame-shift correction for long-read (meta)genomics

srisvs33/SAOB_Metaproteogenomics

Metabolic networks of a syntrophic-acetate oxidizing lab-scale bioreactor community

srisvs33/shasta

De novo assembly from Oxford Nanopore reads.

srisvs33/SprayNPray

Rapid and simple taxonomic profiling of genome and metagenome contigs

srisvs33/stRainy

Graph-based assembly phasing

srisvs33/strainyMAG

ONT pipeline

srisvs33/Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes

srisvs33/wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly