thexiyang Goto Github PK

anhydeg

Database of anaerobic hydrocarbon degradation genes used for functional gene searching of metagenome data sets

bamm

Metagenomics-focused BAM file manipulation

biodata

All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")

bioscripts

some useful scripts for working with genomics and sequencing data

clonalframeml

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

cmseq

Set of utilities on sequences and BAM files

crisprdetect_3.0

ebame18

Long read metagenomics practical at EBAME18

emg-viral-pipeline

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

eukrep

fegenie

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes

graftm

GraftM - Rapid community profiles from metagenomes

grodon

gtotree

A user-friendly workflow for phylogenomics

hamronization

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

handyscripts

Handy scripts I've set aside in case people find them handy

hgtector

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

ls-bsr

Large scale Blast Score Ratio (BSR) analysis

magiccave

A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.

maliampi

Maximum Likelihood Amplicon Pipeline

mcorr

Inferring bacterial recombination rates from large-scale sequencing datasets.

metabolic

A scalable high-throughput metabolic and biogeochemical functional trait profiler

metagenome_analyses

Using IDBA-ud, this is how we assemble metagenomic reads into scaffolds on different projects

metagenome_pfam_score

Protocol for finding informative protein families and then using them to score metagenomic sets.

metagenomics-tutorials

metagenomics_crash_course

metapop

A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations

metawrap

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

midas

An integrated pipeline for estimating strain-level genomic variation from metagenomic data

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.