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Snakebite – Pipelines

An overview of the currently available and published pipelines under the Snakebite framework. There are more under development, so in case you miss one, please be patient, reach out or contribute.

Snakebite – Metagenomics

A pipeline aimed to run metagenomics. Includes metagenome assembly, gene prediction and annotation, creation of MAGs as well as a taxonomic identification and functional interpretation via gene abundances and KEGG pathway enrichments.

Snakebite – GBS

This pipeline runs a complete Genotyping-by-sequencing analysis, rich in features, see details. Works with and without reference genome, provides in-silico predictions and extensive alignment statistics.

Snakebite – miRNA

This pipeline is tailored for the analysis of microRNAs and other small non-coding RNA. It uses the mirbase information, predicts novel miRNA and runs different ‘gene expression’ analyses, PCAs, etc. and also quantifies and analyses tRNA

Snakebite – RNAseq

The pipeline to process mRNA and other transcribed elements. It also runs differently expression analysis, clustering and PCA as well as regular trimming and QC as well as novel gene prediction and a transcriptome assembly.

(Please note, above pictures are not representative for the pipeline itself and just based on a quick search from and should be changed to something more meaningful at some point)