NBIC Galaxy Server: NBIC Pipelines

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On the NBIC Galaxy server and its VM packages, we share the NGS and Proteomics pipelines developed by NBIC staffs. They are all open source tools and freely available. We encourage both internal NBIC and external NBIC members to use it.

GAPSS

Developer: Matthew Hestand & Jeroen Laros

Main features: SNP calling, CAGE/SAGE analysis

Status: Released

Color-space Variant Calling

Developer: Frans Ruzius

Main features: Detect SNP/indel/SNV from color-space input data.

Status: Beta


Narwhal

https://trac.nbic.nl/narwhal/

Developer: Rutger Brouwer

Main features: Alignment, variant calling

Status: Released

Chip-seq Pipeline

Developer: Rutger Brouwer

Main features: Chip-seq study, visualization

Status: Beta

Letter-space Alignment Benchmarking

Developer: Frans Ruzius, Freerk van Dijk, Leon Mei

Main features: Automated benchmarking of alignment software

Status: Beta

Simulated Dataset Generation

Developer: Frans Ruzius, Kai Ye, Leon Mei

Main features: Simulate the output dataset from sequencing machines.

Status: Pre-Alpha

msCompare

Developer: Berend Hoekman

Main features: Mass Spectrum study

Status: Released

De-novo Assembly Benchmarking

Developer: Jan van Haarst, Leon Mei

Main features: run de novo assemblers with benchmarking

Status: Beta