zjyzjjzmt's repositories
AncientMetagenomeDir
Repository containing lists of all published ancient metagenome samples (and related)
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.
emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
Flye
De novo assembler for single molecule sequencing reads using repeat graphs
ggkegg
Analyzing and visualizing KEGG information using the grammar of graphics
iqtree2
NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
Metabuli
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
MGV
Supporting code for uncultivated gut virus manuscript
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
phanta
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
phyloFlash
phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
phylophlan
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
pilon
Pilon is an automated genome assembly improvement and variant detection tool
plsdb
PLSDB pipeline to collect bacterial plasmids from NCBI
raxml-ng
RAxML Next Generation: faster, easier-to-use and more flexible
RESCRIPt
REference Sequence annotation and CuRatIon Pipeline
RiboDetector
Accurate and rapid RiboRNA sequences Detector based on deep learning
RiverMethaneFlux
This is an ongoing project trying to quantify CH4 emissions from rivers in space and time.
run_dbcan
Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
serratus
Ultra-deep search for novel viruses
VIRIDIC
VIRIDIC (Virus Intergenomic Distance Calculator) computes pairwise intergenomic distances/similarities amongst viral genomes.
vRhyme
Binning Virus Genomes from Metagenomes
WMSA
The Multiple Sequence Alignment which developed by Wym6912
YACHT
A mathematically characterized hypothesis test for organism presence/absence in a metagenome