BCCDC-PHL/plasmid-screen BCCDC-PHL/plasmid-screen

  • Stars
    star
    1
  • Language
    Python
  • Created over 3 years ago
  • Updated 5 months ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
BCCDC-PHL/plasmid-screen
github

BCCDC-PHL

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

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

More 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

basic-sequence-qc

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