Pinned Repositories
AncientMetagenomeDir
Repository containing lists of all published ancient metagenome samples (and related)
arg_ranker
biobakery
bioBakery tools for meta'omic profiling
cdhit
Automatically exported from code.google.com/p/cdhit
cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
CheckM
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
cobra
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
DAS_Tool
DAS Tool
diamond
Accelerated BLAST compatible local sequence aligner.
drep
Rapid comparison and dereplication of genomes
zjyzjjzmt's Repositories
zjyzjjzmt/AncientMetagenomeDir
Repository containing lists of all published ancient metagenome samples (and related)
zjyzjjzmt/arg_ranker
zjyzjjzmt/cobra
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
zjyzjjzmt/emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
zjyzjjzmt/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
zjyzjjzmt/fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
zjyzjjzmt/Flye
De novo assembler for single molecule sequencing reads using repeat graphs
zjyzjjzmt/ggkegg
Analyzing and visualizing KEGG information using the grammar of graphics
zjyzjjzmt/iqtree2
NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
zjyzjjzmt/KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
zjyzjjzmt/lovis4u
Bioinformatics tool for Locus Visualisation
zjyzjjzmt/Metabuli
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
zjyzjjzmt/MetaPhage
zjyzjjzmt/mkCOInr
Make a non-redundant, comprehensive COI database from NCBI and BOLD and include customizing options
zjyzjjzmt/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
zjyzjjzmt/phanta
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
zjyzjjzmt/phyloFlash
phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
zjyzjjzmt/pilon
Pilon is an automated genome assembly improvement and variant detection tool
zjyzjjzmt/plsdb
PLSDB pipeline to collect bacterial plasmids from NCBI
zjyzjjzmt/RESCRIPt
REference Sequence annotation and CuRatIon Pipeline
zjyzjjzmt/RiboDetector
Accurate and rapid RiboRNA sequences Detector based on deep learning
zjyzjjzmt/RiverMethaneFlux
This is an ongoing project trying to quantify CH4 emissions from rivers in space and time.
zjyzjjzmt/run_dbcan
Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
zjyzjjzmt/serratus
Ultra-deep search for novel viruses
zjyzjjzmt/standard-RAxML
zjyzjjzmt/vamb
Variational autoencoder for metagenomic binning
zjyzjjzmt/VIRIDIC
VIRIDIC (Virus Intergenomic Distance Calculator) computes pairwise intergenomic distances/similarities amongst viral genomes.
zjyzjjzmt/vRhyme
Binning Virus Genomes from Metagenomes
zjyzjjzmt/WMSA
The Multiple Sequence Alignment which developed by Wym6912
zjyzjjzmt/YACHT
A mathematically characterized hypothesis test for organism presence/absence in a metagenome