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/COMEBin

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/FRAM_STRAIT_WSC20_data_analysis

Long read metagenomics SOP

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/MAGqual

MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards

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/NextDenovo

Fast and accurate de novo assembler for long reads

srisvs33/Norwegian_wild_Salmon_2022

genome resolve metagenomics and comparative genomics to investigate the metagenome dynamics and hologenome of more than 70 adult foraging wild Atlantic salmon. We further compare the microbiotas from Atlantic salmon with gut bacteria of other fish species from Norway to elucidate environmental and host related dynamics.

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/ViWrap

A wrapper to identify, bin, classify, and predict host-viral relationship for viruses

srisvs33/wtdbg2

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