Thomas Cokelaer's Projects
Run assembler (Canu, flye, hifiasm) on a set of long read files
Pipeline to map a set of FastQ files
MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads
Package used to analyse Mass spectrometry data set
Aggregate results from bioinformatics analyses across many samples into a single report.
Mummer alignment tool
Pipeline utility to perform merge of barcoded nanopore runs
pacbio tools
QC on pacbio data
A conda-smithy repository for pykwalify.
Pyodide is a Python distribution for the browser and Node.js based on WebAssembly
Utility to visualise the number of downloads of a package available on Pypi website
Notes and courses about the Python langage
A quality control pipeline for illumina data set. This pipeline removes contaminants (e.g. Phix), performs fastqc, adapter cleaning and trimming and checks for contaminants
Utilities to ease the creation of HTML/PDF reports using Python language
A simple utility to convert a bunch of input fastq files into their reverse complement
Workflow to find ribosomal feature in set of FastQ files
RNA-seq, QC and differential analysis pipeline
Sequana: a set of Snakemake NGS pipelines
The Sequana Wrapper Repository is a collection of reusable wrappers used in Sequana Pipelines.
convert files from one format to another using bioconvert
a cookiecutter sequana pipeline template
A set of tools to help building or using sequana pipelines
Sequanix is a graphical user interface (GUI) that can be used to run Snakemake workflows.
This is the development home of the workflow management system Snakemake. For general information, see
Homepage for the snakemake days in Amsterdam 2017
Spectral Analysis in Python
See README file or jump to