amsyuan

amsyuan's Stars

• Jamalijama/Predict_IAV_Host

  Machine Learning Predicts Human-adaptative Influenza A Viruses Based on Viral Nucleotide Composition

  52

• neherlab/pan-genome-visualization

  Visualization of the pan-genome output by panX

  Language:JavaScript6214

• thomasp85/PanViz

  D3 based visualisation for comparative genomics

  Language:JavaScript142

• thomasp85/PanVizGenerator

  Create your own PanViz visualizations

  Language:R197

• OATML-Markslab/EVEscape

  Official repository for the paper "Learning from pre-pandemic data to forecast viral antibody escape"

  Language:Python519

• dmitropher/af2_multistate_hallucination

  AF2 based MCMC Hallucination Script based on Wicky, Milles, Courbet et al 2022

  Language:Python82

• Peldom/papers_for_protein_design_using_DL

  List of papers about Proteins Design using Deep Learning

  1.5k182

• jianhong/16S_pipeline

  16S RNA microbiome pipeline

  Language:Nextflow6

• sirselim/guppy_parameter_optimiser

  A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate

  Language:Shell314

• rrwick/Long-read-assembler-comparison

  Benchmarking of long-read assembly tools for bacterial whole genomes

  Language:Python17014

• bonsai-team/Porechop_ABI

  Adapter trimmer for Oxford Nanopore reads using ab initio method

  Language:C++384

• nanoporetech/Clair3

  Clair3 - Integrating pileup and full-alignment for high-performance long-read variant calling

  Language:Python51

• nanoporetech/DTR-phage-pipeline

  Language:Python166

• CDCgov/SanitizeMe

  Remove host contaminants from sequencing files

  Language:Python95

• biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE

  A practical guide to build de-novo transcriptome assemblies for non-model organisms (described in Montero-Mendieta et al. 2017).

  2710

• tpoorten/dotPlotly

  Generate an interactive dot plot from mummer or minimap alignments

  Language:HTML19356

• dellytools/delly

  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

  Language:C++451138

• Nextomics/NextDenovo

  Fast and accurate de novo assembler for long reads

  Language:C37353

• wdecoster/nanocomp

  Comparison of multiple long read datasets

  Language:Python1189

• rpetit3/dragonflye

  :dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads

  Language:Perl11910

• lh3/srf

  SRF: Satellite Repeat Finder

  Language:TeX896

• AnantharamanLab/vRhyme

  Binning Virus Genomes from Metagenomes

  Language:Python5910

• fbreitwieser/krakenuniq

  🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

  Language:C++22644

• ukhsa-collaboration/kmerid

  Language:C83

• ukhsa-collaboration/MOST

  Language:Python166

• jordanlab/stringMLST

  Fast k-mer based tool for multi locus sequence typing (MLST)

  Language:Python437

• DaehwanKimLab/centrifuge

  Classifier for metagenomic sequences

  Language:C++25173

• nanoporetech/rerio

  Research release basecalling models and configurations

  Language:Python10310

• timkahlke/LongRead_tutorials

  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data

  12729

• HKU-BAL/Clair3

  Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

  Language:Python25031