danrlu

danrlu's Stars

• nextflow-io/nextflow

  A DSL for data-driven computational pipelines

  Language:Groovy2.7k873.2k622

• plotly/plotly.R

  An interactive graphing library for R

  Language:R2.5k1151.9k622

• OpenGene/fastp

  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

  Language:C++1.9k50517332

• jokergoo/ComplexHeatmap

  Make Complex Heatmaps

  Language:R1.3k341.1k225

• cmdcolin/awesome-genome-visualization

  A list of interesting genome browser or genome-browser-like implementations

  Language:TypeScript835289108

• rrwick/Unicycler

  hybrid assembly pipeline for bacterial genomes

  Language:C++55330328131

• pachterlab/ffq

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

  Language:Python544135047

• fefong/markdown_readme

  Markdown - you can mark up titles, lists, tables, etc., in a much cleaner, readable and accurate way if you do it with HTML.

  489521.8k

• marbl/Mash

  Fast genome and metagenome distance estimation using MinHash

  Language:C++3863316591

• const-ae/ggupset

  Combination matrix axis for 'ggplot2' to create 'UpSet' plots

  Language:R33473721

• kevinsblake/NatParksPalettes

  Color palette package inspired by National Parks

  Language:R230244

• sanger-pathogens/circlator

  A tool to circularize genome assemblies

  Language:Python2302110459

• tseemann/mlst

  :id: Scan contig files against PubMLST typing schemes

  Language:Shell1932313245

• nickjcroucher/gubbins

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

  Language:Python1701118249

• phac-nml/mob-suite

  MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

  Language:Python1181214331

• evogytis/baltic

  baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

  Language:Python93102629

• oschwengers/referenceseeker

  Rapid determination of appropriate reference genomes.

  Language:Python886255

• Wytamma/GISAIDR

  Programmatically interact with the GISAID database.

  Language:R696509

• simonrharris/SKA

  Split Kmer Analysis

  Language:C++6211301

• bacpop/ska.rust

  Split k-mer analysis – version 2

  Language:Rust594384

• kjolley/BIGSdb

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

  Language:Perl57998220

• broadinstitute/viral-pipelines

  viral-ngs: complete pipelines

  Language:WDL53135728

• bioinf-mcb/gisaid-scrapper

  Scrapping tool for GISAID data regarding SARS-CoV-2

  Language:Python4151516

• lskatz/Kalamari

  :octopus: A curated database of completed assemblies with taxonomy IDs

  Language:Perl396283

• CDCgov/mycosnp-nf

  CDCgov/mycosnp-nf

  Language:Nextflow3635933

• oliverSI/GATK4_Best_Practice

  GATK4 Best Practice Nextflow Pipeline

  312029

• bacpop/pp-sketchlib

  Library of sketching functions used by PopPUNK

  Language:C++303517

• peterk87/sublime-nextflow

  Nextflow workflow syntax highlighting and snippets for Sublime Text 4

  Language:Python24465

• corneliusroemer/pango-sequences

  Consensus sequences for each Pango lineage

  Language:Python19571

• boulund/adapter_benchmark

  Benchmarking adapter and quality trimming tools

  Language:Python9311