peterk87/shiptv

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Created over 5 years ago
Updated almost 2 years ago

peterk87/shiptv

peterk87

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Standalone HTML interactive phylogenetic tree visualization powered by Phylocanvas and Javascript

sublime-nextflow

Nextflow workflow syntax highlighting and snippets for Sublime Text 4

nf-flu

Influenza genome analysis Nextflow workflow

filter_classified_reads

Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.

nf-virontus

Oxford Nanopore reference mapping, taxonomic classification, de novo assembly workflow primarily for viral sequence data

nf-villumina

Generic viral Illumina sequence analysis pipeline

irma

Iterative Refinement Meta-Assembler

nf-illmap

Nextflow workflow for Illumina read mapping, variant calling and consensus sequence generation using Snippy

2020-08-20-nextflow-presentation-reveal-cljs

An Intro to Nextflow (2020-08-20)

viral_verify

xlavir

Excel report from bioinformatics analysis of viral seq data with nf-core/viralrecon and other Nextflow workflows

aodp

Automated Oligonucleotide Design Pipeline (AODP) from https://bitbucket.org/wenchen_aafc/aodp_v2.0_release/

sistr_web_analyze

Perform SISTR analysis of genome FASTA files through the SISTR REST API using Python requests

Jupyter Notebook

heidelberg_subtyping

Subtype Salmonella enterica subsp. enterica serovar Heidelberg genomes using an in-silico 33 bp k-mer subtyping method developed by Genevieve Labbe, Roger Johnson, et al from the Public Health Agency of Canada.

nf-cleanplex-preprocess

Nextflow workflow to preprocess and trim primers from Paragon Genomics SARS-CoV-2 CleanPlex Illumina sequence data.

nf-iav-ont

blast2xl

BLAST XLSX Report Creator and Sequence Sorter

irma-singularity

2019-04-08-nextflow-presentation-reveal-cljs

Intro presentation on Nextflow given 2019-04-08