howard-ryan

howard-ryan's Stars

• HughCottingham/clinopore-nf

  ONT-first assembly pipeline

  Language:Python111

• wdecoster/nanocomp

  Comparison of multiple long read datasets

  Language:Python1039

• nanoporetech/dorado

  Oxford Nanopore's Basecaller

  Language:C++50460

• nanoporetech/pod5-file-format

  Pod5: a high performance file format for nanopore reads.

  Language:C++13418

• sc932/ALE

  Assembly Likelihood Estimator

  Language:C327

• outbreak-info/outbreak.info

  During outbreaks of emerging diseases such as COVID-19, efficiently collecting, sharing, and integrating data is critical to scientific research. outbreak.info is a resource to aggregate all this information into a single location.

  Language:Vue3313

• davetang/learning_vcf_file

  Learning the Variant Call Format

  Language:Perl13740

• piyuranjan/SNIKT

  Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bioinformatics/btac389

  Language:HTML172

• cdelahaye/SeqFaiLR

  Analysis of sequencing error profile for long read data.

  Language:Python122

• charmbracelet/glow

  Render markdown on the CLI, with pizzazz! 💅🏻

  Language:Go16.1k352

• koalaman/shellcheck

  ShellCheck, a static analysis tool for shell scripts

  Language:Haskell36.3k1.8k

• akavel/up

  Ultimate Plumber is a tool for writing Linux pipes with instant live preview

  Language:Go8.3k128

• biobakery/MetaPhlAn

  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

  Language:Python29886

• bioinformatics-centre/kaiju

  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

  Language:C26966

• DerrickWood/kraken2

  The second version of the Kraken taxonomic sequence classification system

  Language:C++718270

• fbreitwieser/pavian

  🌈 Interactive analysis of metagenomics data

  Language:R38875

• marbl/Krona

  Interactively explore metagenomes and more from a web browser.

  Language:JavaScript464102

• rrwick/Basecalling-comparison

  A comparison of different Oxford Nanopore basecallers

  Language:Python31354

• alshai/levioSAM

  Lift-over alignments from variant-aware references

  Language:C++344

• philippbayer/submission_checklist

  A checklist to help you avoid all those minor errors when submitting a scientific manuscript

  8612

• jodyphelan/TBProfiler

  Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

  Language:Python10443

• jodyphelan/tbdb

  Standard database for the TBProfiler tool

  Language:Python2818

• julibeg/HHS

  Hungry-Hungry SNPos

  Language:Rust11

• asmngs/asmngs20

  ASMNGS20 - 2020 Conference Details

  156

• CDCgov/SARS-CoV-2_Sequencing

  A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

  Language:Perl34583

• artic-network/rampart

  Read Assignment, Mapping, and Phylogenetic Analysis in Real Time

  Language:JavaScript7934

• artic-network/civet

  Cluster Investigation & Virus Epidemiology Tool

  Language:Python4814

• nextstrain/augur

  Pipeline components for real-time phylodynamic analysis

  Language:Python268129

• SamStudio8/majora2

  Malleable All-seeing Journal Of Research Artifacts

  Language:Python367

• UPHL-BioNGS/Cecret

  Reference-based consensus creation

  Language:Nextflow5026