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Yan Shao (ys4)

ys4

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Company:Wellcome Trust Sanger Institute

Location:Cambridge, UK

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Yan Shao's starred repositories

wf-bacterial-genomes

Small variant calling for haploid samples

Language:PythonLicense:NOASSERTIONStargazers:21Issues:0Issues:0

iNEXT

R package for interpolation and extrapolation

Language:RStargazers:57Issues:0Issues:0

latinbiota

Central repository with scripts and workflows for the analysis of the gut microbiome of the Latinbiota cohort

Language:RLicense:MITStargazers:3Issues:0Issues:0

NanoPlot

Plotting scripts for long read sequencing data

Language:PythonLicense:MITStargazers:407Issues:0Issues:0

Polypolish

a short-read polishing tool for long-read assemblies

Language:RustLicense:GPL-3.0Stargazers:140Issues:0Issues:0

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Language:PythonLicense:GPL-3.0Stargazers:423Issues:0Issues:0

gunc

Python package for detection of chimerism and contamination in prokaryotic genomes.

Language:PythonLicense:GPL-3.0Stargazers:63Issues:0Issues:0

alphafold

Open source code for AlphaFold.

Language:PythonLicense:Apache-2.0Stargazers:12214Issues:0Issues:0

ffq

A tool to find sequencing data and metadata from public databases.

Language:PythonLicense:MITStargazers:538Issues:0Issues:0

medaka

Sequence correction provided by ONT Research

Language:PythonLicense:NOASSERTIONStargazers:400Issues:0Issues:0

Flye

De novo assembler for single molecule sequencing reads using repeat graphs

Language:CLicense:NOASSERTIONStargazers:758Issues:0Issues:0

Porechop

adapter trimmer for Oxford Nanopore reads

Language:C++License:GPL-3.0Stargazers:327Issues:0Issues:0

Unicycler

hybrid assembly pipeline for bacterial genomes

Language:C++License:GPL-3.0Stargazers:546Issues:0Issues:0

CoverM

Read coverage calculator for metagenomics

Language:RustLicense:GPL-3.0Stargazers:285Issues:0Issues:0

BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

Language:PerlLicense:NOASSERTIONStargazers:343Issues:0Issues:0

EukDetect

Language:PythonLicense:MITStargazers:41Issues:0Issues:0

genome_updater

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

Language:ShellLicense:MITStargazers:137Issues:0Issues:0

GToTree

A user-friendly workflow for phylogenomics

Language:ShellLicense:GPL-3.0Stargazers:197Issues:0Issues:0

R-graph-gallery

A website that displays hundreds of R charts with their code

Language:HTMLLicense:MITStargazers:661Issues:0Issues:0

animalcules

R shiny app for interactive microbiome analysis

Language:RLicense:NOASSERTIONStargazers:51Issues:0Issues:0

genomes-catalogue-pipeline

MGnify genome analysis pipeline

Language:PythonLicense:NOASSERTIONStargazers:96Issues:0Issues:0

serratus

Ultra-deep search for novel viruses

Language:Jupyter NotebookLicense:GPL-3.0Stargazers:253Issues:0Issues:0

VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data

Language:PythonLicense:GPL-2.0Stargazers:207Issues:0Issues:0

Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes

Language:PythonLicense:GPL-3.0Stargazers:303Issues:0Issues:0

enrichM

Toolbox for comparative genomics of MAGs

Language:PythonStargazers:81Issues:0Issues:0

Prodigal

Prodigal Gene Prediction Software

Language:CLicense:GPL-3.0Stargazers:430Issues:0Issues:0

DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Language:PythonLicense:GPL-3.0Stargazers:240Issues:0Issues:0

IQ-TREE

Efficient phylogenomic software by maximum likelihood

Language:C++License:GPL-2.0Stargazers:183Issues:0Issues:0

grabseqs

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

Language:PythonLicense:MITStargazers:103Issues:0Issues:0

cmseq

Set of utilities on sequences and BAM files

Language:PythonLicense:MITStargazers:24Issues:0Issues:0