Hua-clearlabs

Hua-clearlabs's Stars

• nickjcroucher/gubbins

  Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

  Language:Python16049

• bacpop/ggCaller

  Bifrost graph gene caller.

  Language:C++856

• retorquere/zotero-better-bibtex

  Make Zotero effective for us LaTeX holdouts

  Language:TypeScript5k278

• theiagen/public_health_bacterial_genomics

  Language:WDL2614

• INSaFLU/INSaFLU

  INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomic surveillance

  Language:Python3011

• almiheenko/AGB

  Interactive visualization of assembly graphs

  Language:JavaScript777

• theiagen/public_health_viral_genomics

  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2

  Language:WDL3817

• alliblk/genepi-book

  Language:CSS163

• dockstore/dockstore

  Our VM/Docker sharing infrastructure and management component

  Language:Java11627

• BU-ISCIII/plasmidID

  PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

  Language:Shell378

• nf-core/viralrecon

  Assembly and intrahost/low-frequency variant calling for viral samples

  Language:Nextflow112104

• shiquan/bamdst

  a lightweight bam file depth statistical tool

  Language:C14548

• rrwick/Deepbinner

  a signal-level demultiplexer for Oxford Nanopore reads

  Language:Python12423

• parklab/bamsnap

  Language:HTML10822

• bwa-mem2/bwa-mem2

  The next version of bwa-mem

  Language:C++69893

• ncbi/vadr

  Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation

  Language:Perl9322

• nextstrain/nextclade

  Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

  Language:Rust20458

• jeffdaily/parasail

  Pairwise Sequence Alignment Library

  Language:C24034

• aresti/primalscheme

  a tool for designing primer panels for multiplex PCR.

  Language:Python9132

• andersen-lab/ivar

  iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

  Language:C++11539

• xavierdidelot/ClonalFrameML

  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

  Language:C++10326

• kjolley/BIGSdb

  Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

  Language:Perl5619

• ncbi/sra-human-scrubber

  An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.

  Language:Shell425

• virus-evolution/gofasta

  Language:Go321

• cov-lineages/pangoLEARN

  Store of the trained model for pangolin to access.

  Language:PureBasic5513

• denglab/SeqSero2

  SeqSero2

  Language:Python3217

• andersen-lab/Freyja

  Depth-weighted De-Mixing

  Language:HTML10029

• broadinstitute/viral-pipelines

  viral-ngs: complete pipelines

  Language:WDL5128

• tseemann/noary

  🍣 🦐 A lightweight nucleotide bacterial ortholog clustering tool

  Language:Perl72

• rrwick/Polypolish

  a short-read polishing tool for long-read assemblies

  Language:Rust1379