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16s-nf

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

abritamr

A pipeline for running AMRfinderPlus and collating results into functional classes

align-compare

Pipeline to make pairwise comparisons of matched fasta sequences.

alignment-variants

Pipeline to perform alignment & variant calling on whole-genome sequence data

amplicon-consensus

amplicone

analysis-automation

artic-mpxv2022

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

auspice

Web app for visualizing pathogen evolution

auto-combine-nanopore-fastq

Automated combining of fastq files from Oxford Nanopore sequencing runs

auto-cpo

Automation of Genomic Analyses for Carbapenemase-Producing Organisms (CPOs)

auto-fastq-symlink

Automated symlinking of sequence data

auto-flu

Automated analysis of flu sequence data using BCCDC-PHL/FluViewer_nf

auto-hcv

Automated genomic analysis of HCV sequence data

auto-illumina-run-qc-check

Automated Primary Sequence QC Checks for Illumina Sequencing Runs

auto-irida-azure-upload

Automated upload of sequence data to IRIDA platform

auto-irida-uploader

Automated uploading of sequence data into IRIDA instances, used in conjunction with auto-irida-azure-upload

auto-ncov

Automated genomic analysis of SARS-CoV-2 sequence data

auto-pangolin

Automated lineage assignment of SARS-CoV-2 sequences with pangolin

auto-routine-nanopore-qc

auto-routine-sequence-qc

auto-tb-amr-amplicon

basic-nanopore-qc

Collect basic sequence QC metrics from nanopore reads

basic-sequence-qc

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

biohansel-nf

Nextflow wrapper for biohansel

blast-reads

BLAST a set of fastq reads against a database

call-variants

Align against a reference genome and call variants

cgmlst-clustering

Scripts to support clustering of cgMLST allele profiles

chewbbaca-nf