Explore projects

This workflow will use a pseudo aligner (Kallisto or Salmon) to quantify transcript abundance and test for differential expression.

Comparison of multiple bioinformatic programs for each step of eDNA analysis

Codes for the paper : "Genomic resources for Mediterranean fishes"

Some basic tests to check websites :

https certificates, checksum of the index web page, HTTP answers.

Seek positions of variants onto genome and check if they are on an annotated region e.g. coding region. Then seek the proteic function of the gene

This project is aimed at providing a list of "Ethical' journals where ISEM's researchers are used to publishing there works.

This project presents a pipeline based on OBITools commands in order to eliminate sequences interpreted as coming from PCR errors and to assign each remaining sequence to a taxon thanks to a reference database.

Analysis around palinurus ortus

This project is based on the idea that gathering similar sequences allows to faithfully study them by eliminating sequences generated from PCR or NGS errors.

OTU clustering with SWARM on RAPIDRUN data encapsulated in SNAKEMAKE

This project has for goal to filtrate efficiently eDNA sequences after PCR amplification and NGS, in order to eliminate the false sequences generated by these technologies.

Codes Pierre-Edouard Guerin wrote for the scientific paper "Predicting genotype environmental range from genome–environment associations"

Here is a version of the pipeline "only_obitools" using nextflow, a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data.

Here, we reproduce the bioinformatics pipeline used by SPYGEN to generate species environmental presence from raw eDNA data.

Data for the tutorial on how to analyze DNA metabarcoding data produced on Illumina sequencers

Simulations of metabarcoding data from fish 12S Teleo1