yananzh

Pinned Repositories

ads1-notebooks
Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing
Language:Jupyter Notebook0 1 00
Algorithms-for-DNA-Sequencing
Coursera MOOC Algorithms for DNA Sequencing by Ben Langmead, PhD, Jacob Pritt
Language:Python0 1 00
amr
amr_finder
Language:C++0 1 00
AppliedGenomeResearch
course about NGS data processing: genomics and transcriptomics
Language:Python0 1 00
ariba
Antimicrobial Resistance Identification By Assembly
Language:Python0 1 00
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
00
bactopia
A flexible pipeline for complete analysis of bacterial genomes
Language:Nextflow0 1 00
BCB546_Spring2023
Materials for EEOB/BCB546: Bioinformatics data skills
Language:Jupyter Notebook0 0 00
bds-files
Supplementary files for my book, "Bioinformatics Data Skills"
Language:Python0 1 00
bioinformatics
An Introductory Undergraduate course in Bioinformatics
Language:R0 1 00

yananzh's Repositories

yananzh/amr
amr_finder
Language:C++0 1 00
yananzh/ariba
Antimicrobial Resistance Identification By Assembly
Language:Python0 1 00
yananzh/bactopia
A flexible pipeline for complete analysis of bacterial genomes
Language:Nextflow0 1 00
yananzh/BCB546_Spring2023
Materials for EEOB/BCB546: Bioinformatics data skills
Language:Jupyter Notebook0 0 00
yananzh/Bioinformatics-with-Python-Cookbook-Second-Edition
Bioinformatics with Python Cookbook Second Edition, published by Packt
Language:OpenEdge ABL1 0
yananzh/CheckM
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Language:Python1 0
yananzh/data-science-at-the-command-line
Data Science at the Command Line
Language:HTML1 0
yananzh/diamond
Accelerated BLAST compatible local sequence aligner.
Language:C++1 0
yananzh/Flye
De novo assembler for single molecule sequencing reads using repeat graphs
Language:C1 0
yananzh/gggenomes
A grammar of graphics for comparative genomics
Language:R1 0
yananzh/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Language:Python1 0
yananzh/helpful_commands
Command-line tools, commands, and code snippets for performing routine data processing and bioinformatics tasks
1 0
yananzh/ISEScan
A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
Language:Python1 0
yananzh/jupyterlab-desktop
JupyterLab desktop application, based on Electron.
Language:TypeScript1 0
yananzh/macsyfinder
MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.
Language:Python1 0
yananzh/mcorr
Inferring bacterial recombination rates from large-scale sequencing datasets.
Language:Go1 0
yananzh/MicrobeAnnotator
Pipeline for metabolic annotation of microbial genomes
yananzh/panaroo
An updated pipeline for pangenome investigation
yananzh/pgap
NCBI Prokaryotic Genome Annotation Pipeline
yananzh/phylophlan
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
Language:Python1 0
yananzh/phyml
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
Language:C1 0
yananzh/Polypolish
a short-read polishing tool for long-read assemblies
Language:Python1 0
yananzh/PopPUNK
PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
yananzh/prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
Language:Perl1 0
yananzh/pyani
Application and Python module for average nucleotide identity analyses of microbes.
Language:Python1 0
yananzh/pyseer
SEER, reimplemented in python 🐍🔮
Language:Python1 0
yananzh/raven
De novo genome assembler for long uncorrected reads
Language:C++1 0
yananzh/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Language:Perl1 0
yananzh/SuperCRUNCH
A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and/or local sequence data.
yananzh/Trycycler
A tool for generating consensus long-read assemblies for bacterial genomes
Language:Python1 0