BC Centre for Disease Control Public Health Laboratory (@BCCDC-PHL)
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BCCDC-PHL

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  • Stars
    star
    82
  • Global Org. Rank 63,385 (Top 21 %)
  • Registered over 4 years ago
  • Most used languages
    Python
         56.8 %
    Nextflow     37.8 %
    C
         2.7 %
    Clojure
         2.7 %
  • Location 🇨🇦 Canada
  • Country Total Rank 7,710
  • Country Ranking
    Nextflow     2
    Clojure
         143
    Python
         2,071
    C
         2,201

Top repositories

1

simulate-short-reads

Generate simulated illumina sequence reads from a reference sequence
Nextflow
5
star
2

taxon-abundance

Python
5
star
3

fluflo

Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.
Nextflow
5
star
4

WasteFlow

Nextflow pipeline for pathogen surveillance in wastewater
Nextflow
4
star
5

tbprofiler-nf

Nextflow Wrapper for TBProfiler
Python
4
star
6

dragonflye-nf

Nextflow wrapper for the dragonflye assembler, with additional QC
Nextflow
4
star
7

simulate-long-reads

Generate simulated oxford nanopore reads from a reference sequence
Nextflow
4
star
8

tb-db

Database for storage of M. tuberculosis genomics analysis results
Python
3
star
9

kma-cgmlst

A cgMLST pipeline based on the KMA aligner
Nextflow
3
star
10

cgmlst-clustering

Scripts to support clustering of cgMLST allele profiles
C
3
star
11

vcf-diff

Check for differences between two vcf files
Python
3
star
12

covid-qc

Static site for displaying COVID-19 sequencing quality control data
Clojure
3
star
13

illumina-uploader

Watch for new files in Illumina sequencer and upload to remote server
Python
2
star
14

covflo

Nextflow pipeline for generation of BCCDC routine SARS-CoV-2 phylogenetic trees to be visualized with Auspice.
Python
2
star
15

ncov-tools-nf

A nextflow-based workflow for running ncov-tools
Nextflow
2
star
16

16s-nf

Prepare a report for taxonomic assignment based on 16S rRNA sequences, using BLAST.
Python
2
star
17

routine-sequence-qc

Pipeline for running routine quality control analyses on illumina sequence data
Python
1
star
18

hcv-nf

Genomic analysis pipeline for genotyping of Hepatitis C Virus
Python
1
star
19

pangolin-nf

Run pangolin on multiple output directories from BCCDC-PHL/ncov2019-artic-nf
Nextflow
1
star
20

auto-flu

Automated analysis of flu sequence data using BCCDC-PHL/fluviewer-nf
Python
1
star
21

blast-reads

BLAST a set of fastq reads against a database
Nextflow
1
star
22

type-variants-nf

Detect SARS-CoV-2 variants using outputs from the ncov2019-artic-nf pipeline
Python
1
star
23

mpxv-qc

Companion pipeline to perform quality control for BCCDC-PHL/mpxv-artic-nf
Python
1
star
24

routine-assembly

Pipeline for performing routine genome assembly
Nextflow
1
star
25

auto-illumina-run-qc-check

Automated Primary Sequence QC Checks for Illumina Sequencing Runs
Python
1
star
26

demultiplex-nanopore

Demultiplex nanopore reads and combine into a single file per sample
Nextflow
1
star
27

auto-ncov

Automated genomic analysis of SARS-CoV-2 sequence data
Python
1
star
28

rapid

RAPID Analysis and Processing of Incoming Data
Python
1
star
29

mpxv-artic-nf

Python
1
star
30

auto-irida-upload

Automated upload of sequence data to IRIDA platform
Python
1
star
31

snippy-core-phylogenomics

Nextflow
1
star
32

degrade-fastq

A tool for artificially degrading the quality of fastq files
Python
1
star
33

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.
Python
1
star
34

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
Nextflow
1
star
35

mlst-nf

Run mlst on multiple samples with integrated quality control.
Nextflow
1
star
36

plasmid-screen

Screen plasmids for carbapenemase resistance genes, and classify using MOB Suite
Python
1
star
37

basic-sequence-qc

Generate some basic quality control statistics on an arbitrary set of illumina fastq sequence files.
Python
1
star