Infectieziekteonderzoek, Diagnostiek en laboratorium Surveillance-Bioinformatics (RIVM, The Netherlands) (@RIVM-bioinformatics)
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RIVM-bioinformatics

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Top repositories

1

AmpliGone

A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment
Python
6
star
2

SARS2seq

SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.
Python
6
star
3

TrueConsense

TrueConsense is a consensus caller for viral-targets that create biologically correct consensus sequences. TrueConsense keeps track of open reading frames, compensates for common sequencing or alignment artefacts, and is able to generate consensus sequences on multiple coverage-thresholds at the same time
Python
5
star
4

auriclass

Quick estimation of Candida auris clade using mash
Python
5
star
5

juno-typing

Pipeline to perform bacterial typing (7-locus MLST and serotyping when appropriate). It works with several (but not all) species/genera.
Python
4
star
6

ViroConstrictor

ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome
Python
4
star
7

juno-assembly

Pipeline to process raw sequencing data up to de-novo assembly and the accompanying statistics
Python
3
star
8

HERA-Bioinformatics-Training

Jupyter Notebook
2
star
9

clcbioformatter

Re-formatting Fasta headers to fit CLC bio. Requested by the AMR group.
Python
1
star
10

Juno-annotation

Annotation of chromosomes and plasmids of bacteria (AMR group)
Python
1
star
11

juno-mapping

Reference-based mapping Juno pipeline
Python
1
star
12

Myco_lofreq

Pipeline to call minority variants in Mycobacterium samples
Python
1
star
13

juno-blast

Automated BLASTing from fasta files.
Python
1
star
14

containers

Creating and uploading containers to ghcr
Dockerfile
1
star
15

juno-amr

-
Python
1
star
16

AminoExtract

AminoExtract is a tool for translating and extracting amino acid sequences from nucleotide-sequences based on a GFF input
Python
1
star
17

juno-cgmlst

Pipeline to perform cgMLST (or wgMLST) analysis. At the moment it just handles few genera for cgMLST
Python
1
star