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simulate-short-reads
Generate simulated illumina sequence reads from a reference sequencetaxon-abundance
WasteFlow
Nextflow pipeline for pathogen surveillance in wastewatertbprofiler-nf
Nextflow Wrapper for TBProfilerdragonflye-nf
Nextflow wrapper for the dragonflye assembler, with additional QCsimulate-long-reads
Generate simulated oxford nanopore reads from a reference sequencetb-db
Database for storage of M. tuberculosis genomics analysis resultskma-cgmlst
A cgMLST pipeline based on the KMA alignercgmlst-clustering
Scripts to support clustering of cgMLST allele profilesvcf-diff
Check for differences between two vcf filescovid-qc
Static site for displaying COVID-19 sequencing quality control dataillumina-uploader
Watch for new files in Illumina sequencer and upload to remote servercovflo
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-tools16s-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 datahcv-nf
Genomic analysis pipeline for genotyping of Hepatitis C Viruspangolin-nf
Run pangolin on multiple output directories from BCCDC-PHL/ncov2019-artic-nfauto-flu
Automated analysis of flu sequence data using BCCDC-PHL/fluviewer-nfblast-reads
BLAST a set of fastq reads against a databasetype-variants-nf
Detect SARS-CoV-2 variants using outputs from the ncov2019-artic-nf pipelinempxv-qc
Companion pipeline to perform quality control for BCCDC-PHL/mpxv-artic-nfroutine-assembly
Pipeline for performing routine genome assemblyauto-illumina-run-qc-check
Automated Primary Sequence QC Checks for Illumina Sequencing Runsdemultiplex-nanopore
Demultiplex nanopore reads and combine into a single file per sampleauto-ncov
Automated genomic analysis of SARS-CoV-2 sequence datarapid
RAPID Analysis and Processing of Incoming Datampxv-artic-nf
auto-irida-upload
Automated upload of sequence data to IRIDA platformsnippy-core-phylogenomics
degrade-fastq
A tool for artificially degrading the quality of fastq filesillumina-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/Brackenmlst-nf
Run mlst on multiple samples with integrated quality control.plasmid-screen
Screen plasmids for carbapenemase resistance genes, and classify using MOB Suitebasic-sequence-qc
Generate some basic quality control statistics on an arbitrary set of illumina fastq sequence files.Love Open Source and this site? Check out how you can help us