Peter Kruczkiewicz's repositories
2020-08-20-nextflow-presentation-reveal-cljs
An Intro to Nextflow (2020-08-20)
2019-04-08-nextflow-presentation-reveal-cljs
Intro presentation on Nextflow given 2019-04-08
nf-cleanplex-preprocess
Nextflow workflow to preprocess and trim primers from Paragon Genomics SARS-CoV-2 CleanPlex Illumina sequence data.
biohansel
Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes
docker-iqtree
IQ-TREE Alpine Docker container
docker-minknow
Install and run Oxford Nanopore's MinKNOW software on other Linux distros
docker-tvc-tmap-torrent-suite
Docker container for compiled TMAP and TVC tools from the Thermo Fisher Ion Torrent Suite
fast5watch
Nanopore run watcher
genotyphi
Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
ggstatsplot
Enhancing `ggplot2` plots with statistical analysis 📊🎨📣
irida-uploader
Sequence file uploader for IRIDA
Metalign
Metalign: efficient alignment-based metagenomic profiling via containment min hash
nf-bh-typing-comparison
Nextflow workflow to benchmark biohansel, SKA, genotyphi and tb-profiler
nf-biohansel-sra-benchmark
Nextflow workflow for benchmarking biohansel and Snippy with NCBI SRA genomes
nf-centrifuge-build
Nextflow workflow to build a Centrifuge index
pangolin
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
pyahocorasick-feedstock
A conda-smithy repository for pyahocorasick.
snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Unicycler
hybrid assembly pipeline for bacterial genomes
viral-ampliseq-assembly
Snakemake workflow for analysis and assembly of viral genomes from IonTorrent AmpliSeq data.
virtool
Viral infection diagnostics using next-generation sequencing