Netherlands Institute of Ecology (NIOO-KNAW)

Netherlands Institute of Ecology (NIOO-KNAW)'s repositories

epiGBS2

This is the epiGBS2 snakemake pipeline as published in a preprint version.

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2019-02-05-wageningen-genomics

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BSAnalyser is a pipeline designed to benchmark multiple BS aligners and SNP callers from raw BS sequencing data input. It will align sequences using the chosen aligners and call SNPs using the chosen SNP calling tools for each aligner used.

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epiGBS

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epiGBS-pipeline

modified clone from https://github.com/thomasvangurp/epiGBS. Added wrapper scripts and conda compatibility

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HFC-permutation

pipeline for HFC calculations from ped and map file, including permutations

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hydra

Pipeline for amplicon sequencing projects. OTUs can be build with various methods (usearch,vsearch,uparse,swarm) and classified using the RDP Classifier and SINA. Final output is a BIOM file for downstream processing (Phyloseq/R)

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