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Hi there

  • šŸ”­ Iā€™m currently actively working on Sequana and also maintaining BioServices, Damona, Fitter, colormap, spectrum, Bioconvert and easydev.
  • I'm currently leading the bioinformatics and data management activities of the Biomics NGS platform (biomics.pasteur.fr) building pipelines and tools for production.
  • šŸ‘Æ Iā€™m looking to collaborate on BioConvert, BioServices and Damona and of course Sequana. Would you be interested to take the lead on Spectrum, fitter, colormap, please let me know.

Thomas Cokelaer's Projects

lora icon lora

Run assembler (Canu, flye, hifiasm) on a set of long read files

mapper icon mapper

Pipeline to map a set of FastQ files

mecat icon mecat

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

msdas icon msdas

Package used to analyse Mass spectrometry data set

multiqc icon multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

nanomerge icon nanomerge

Pipeline utility to perform merge of barcoded nanopore runs

pyodide icon pyodide

Pyodide is a Python distribution for the browser and Node.js based on WebAssembly

pypiview icon pypiview

Utility to visualise the number of downloads of a package available on Pypi website

quality_control icon quality_control

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

reports icon reports

Utilities to ease the creation of HTML/PDF reports using Python language

revcomp icon revcomp

A simple utility to convert a bunch of input fastq files into their reverse complement

ribofinder icon ribofinder

Workflow to find ribosomal feature in set of FastQ files

rnaseq icon rnaseq

RNA-seq, QC and differential analysis pipeline

sequana icon sequana

Sequana: a set of Snakemake NGS pipelines

sequana-wrappers icon sequana-wrappers

The Sequana Wrapper Repository is a collection of reusable wrappers used in Sequana Pipelines.

sequanix icon sequanix

Sequanix is a graphical user interface (GUI) that can be used to run Snakemake workflows.

snakemake icon snakemake

This is the development home of the workflow management system Snakemake. For general information, see

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