Hua-clearlabs

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zotero-better-bibtex

Make Zotero effective for us LaTeX holdouts

Language:TypeScriptMIT5163 47 2168

bwa-mem2

The next version of bwa-mem

Language:C++NOASSERTION710 36 213

parasail

Pairwise Sequence Alignment Library

Language:CNOASSERTION241 18 94

nextclade

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

Language:RustMIT211 19 448

gubbins

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

Language:PythonGPL-2.0166 13 181

bamdst

a lightweight bam file depth statistical tool

Language:CNOASSERTION146 7 37

Polypolish

a short-read polishing tool for long-read assemblies

Language:RustGPL-3.0142 11 22

Deepbinner

a signal-level demultiplexer for Oxford Nanopore reads

Language:PythonGPL-3.0124 9 39

dockstore

An app store for scientific workflows, tools, notebooks, and services

Language:JavaApache-2.0118 22 3469

ivar

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

Language:C++GPL-3.0115 13 128

viralrecon

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

Language:NextflowMIT113 100 161

bamsnap

Language:HTMLMIT110 9 29

ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

Language:C++GPL-3.0104 10 150

Freyja

Depth-weighted De-Mixing

Language:HTMLBSD-2-Clause100 13 140

vadr

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

Language:PerlNOASSERTION97 19 76

primalscheme

a tool for designing primer panels for multiplex PCR.

Language:PythonGPL-3.094 7 37

ggCaller

Bifrost graph gene caller.

Language:C++MIT86 3 28

AGB

Interactive visualization of assembly graphs

Language:JavaScriptNOASSERTION78 6 12

BIGSdb

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

Language:PerlNOASSERTION56 9 979

pangoLEARN

Store of the trained model for pangolin to access.

Language:PureBasicGPL-3.055 31 37

viral-pipelines

viral-ngs: complete pipelines

Language:WDLNOASSERTION51 13 57

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:ShellNOASSERTION43 25 23

public_health_viral_genomics

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

Language:WDLAGPL-3.039 6 103

plasmidID

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

Language:ShellGPL-3.037 4 24

SeqSero2

SeqSero2

Language:PythonNOASSERTION33 9 42

gofasta

Language:GoMIT31 6 24

INSaFLU

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

Language:PythonGPL-3.030 6 5

public_health_bacterial_genomics

Language:WDLAGPL-3.026 5 109

genepi-book

Language:CSSCC0-1.017 2 2

noary

🍣 🦐 A lightweight nucleotide bacterial ortholog clustering tool

Language:PerlGPL-3.07 3 1