chopper 0.10.0b-GCCcore-12.3.0

Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file. Filtering is done on average read quality and minimal or maximal read length, and applying a headcrop (start of read) and tailcrop (end of read) while printing the reads passing the filter.

Accessing chopper 0.10.0b-GCCcore-12.3.0

To load the module for chopper 0.10.0b-GCCcore-12.3.0 please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):

📋 module load bear-apps/2023a
module load chopper/0.10.0b-GCCcore-12.3.0

BEAR Apps Version

2023a

Architectures

EL8-icelake — EL8-sapphirerapids

The listed architectures consist of two parts: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

More Information

For more information visit the chopper website.

Dependencies

This version of chopper has a direct dependency on: bzip2/1.0.8-GCCcore-12.3.0 GCCcore/12.3.0 XZ/5.4.2-GCCcore-12.3.0

Last modified on 1st May 2025