BCCDC-PHL/snippy-core-phylogenomics

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Created about 4 years ago
Updated 7 months ago

BCCDC-PHL/snippy-core-phylogenomics

BCCDC-PHL

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simulate-short-reads

Generate simulated illumina sequence reads from a reference sequence

taxon-abundance

fluflo

Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.

WasteFlow

Nextflow pipeline for pathogen surveillance in wastewater

tbprofiler-nf

Nextflow Wrapper for TBProfiler

dragonflye-nf

Nextflow wrapper for the dragonflye assembler, with additional QC

simulate-long-reads

Generate simulated oxford nanopore reads from a reference sequence

tb-db

Database for storage of M. tuberculosis genomics analysis results

kma-cgmlst

A cgMLST pipeline based on the KMA aligner

cgmlst-clustering

Scripts to support clustering of cgMLST allele profiles

vcf-diff

Check for differences between two vcf files

covid-qc

Static site for displaying COVID-19 sequencing quality control data

illumina-uploader

Watch for new files in Illumina sequencer and upload to remote server

covflo

Nextflow pipeline for generation of BCCDC routine SARS-CoV-2 phylogenetic trees to be visualized with Auspice.

ncov-tools-nf

A nextflow-based workflow for running ncov-tools

16s-nf

Prepare a report for taxonomic assignment based on 16S rRNA sequences, using BLAST.

routine-sequence-qc

Pipeline for running routine quality control analyses on illumina sequence data

hcv-nf

Genomic analysis pipeline for genotyping of Hepatitis C Virus

pangolin-nf

Run pangolin on multiple output directories from BCCDC-PHL/ncov2019-artic-nf

auto-flu

Automated analysis of flu sequence data using BCCDC-PHL/fluviewer-nf

blast-reads

BLAST a set of fastq reads against a database

type-variants-nf

Detect SARS-CoV-2 variants using outputs from the ncov2019-artic-nf pipeline

mpxv-qc

Companion pipeline to perform quality control for BCCDC-PHL/mpxv-artic-nf

routine-assembly

Pipeline for performing routine genome assembly

auto-illumina-run-qc-check

Automated Primary Sequence QC Checks for Illumina Sequencing Runs

demultiplex-nanopore

Demultiplex nanopore reads and combine into a single file per sample

auto-ncov

Automated genomic analysis of SARS-CoV-2 sequence data

rapid

RAPID Analysis and Processing of Incoming Data

mpxv-artic-nf

auto-irida-upload

Automated upload of sequence data to IRIDA platform

degrade-fastq

A tool for artificially degrading the quality of fastq files

illumina-run-publisher

Watch directories for the creation of illumina sequencer outputs. When detected, publish messages with details of the run to a TCP socket.

dehost-and-verify-illumina

Remove host reads from a microbial pathogen sequence dataset by aligning against a reference genome. Verify that the reads were removed using Kraken2/Bracken

mlst-nf

Run mlst on multiple samples with integrated quality control.

plasmid-screen

Screen plasmids for carbapenemase resistance genes, and classify using MOB Suite

basic-sequence-qc

Generate some basic quality control statistics on an arbitrary set of illumina fastq sequence files.