Adrien Leger

pycoQC. pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

NanoCount. EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2

pycoMeth. DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

NanopolishComp. NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files

MetaCompore. Metacompore is a snakemake pipeline running multiple RNA modifications detection tools for nanopore directRNA sequencing

pycoSnake. pycoSnake is a neatly wrapped collection of snakemake workflows for analysing nanopore and Illumina sequencing data

Chimera_Finder. These BASH script allow to extract chimeric pairs and chimeric reads from NGS data mixing 2 DNA references

ContaVect. Complete suite to analyse DNA contaminants of virus/vector preparation from NGS data

pyBioTools. Collection of tools to manipulate Bioinformatic standard file format + Generic file related function collection

JupyterGenoViewer. JGV is a Python3 package for an embed genomic viewer in Jupyter notebook

blastpy3. Simple and lightweight Python 3 wrapper module for NCBI BLAST+

Sekator. Multithreaded quality and adapter trimmer for PAIRED fastq files (Python2.7/Cython/C)

Quade. Demultiplexer for PAIRED fastq files based on index sequence and PHRED quality (pure python)

MirStat. Simple tool to analyze miRNA QPCR data

fastq_control_sampler. Generates control fastq files R1 and R2 from fasta reference sequences

versipy. Versatile version and medatada managment across the python packaging ecosystem with git integration

nanocompore_paper_analyses. Analyses performed for the nanocompore paper

Fast5Tools. Tools to manipulate Fast5 files

pyBioPlot. High level library for Python 3 containing functions to generate specific plot for NGS and other biology related datasets.

pyScripts. Contains misc data specific python3 scripts

RScripts. Contains misc data specific R-cran scripts

TargetPredict. Predict the targets of a short RNA in annotated features from genomic DNA, using BLAST, MIRANDA...

py_NGS_tools. Collection of undocumented and experimental python tools related to NDS data

pyFastq. Simple python 2.7 librarie to parse fastq files and handle illumina 1.8+ fastq sequences

Find_overlap_reads. Parse a BAM file and extract reads ovelapping given genomic coordinates

BASH_NGS_Tools. Collection of simple NGS tools

pyDNA. Collection of python 2.7 Utilities and Wrapper for DNA / NGS data manipulation

Isis. ISIS generates random insertion sites of a given viral DNA in an host DNA and output Fastq Files

IsFinder. IsFinder find virus insertion site in host genomic DNA from pair end NGS data