CRAMINO¶
CRAMINO can be used to assess the quality of CRAM and BAM files, intended for long read sequencing. The bundle packages version 1.1.0.
Usage example¶
The following command can be executed in the terminal to load the bundle:
The module makes the cramino command available. The cramino_shell command
can be used to access a shell in the bundle.
Run pet list -t cramino for a list of examples. The example was taken from
Biowulf.
Performance notes¶
No performance notes available
Recommended resources per session¶
CRAMINO should be run on a system with at least 4 GB of RAM and 4 threads. According to the documentation: the default number of threads are 4 and a 140Gbase BAM file is processed in 12 minutes, using less than 1Gbyte of memory.
Benchmarks¶
No benchmarks available.
Community guides and tutorials¶
- No community guides available.
Official site and documentation¶
Licensing information¶
CRAMINO is licensed under the MIT license.
Primary citation¶
NanoPack2: population-scale evaluation of long-read sequencing data Open Access Wouter De Coster , Rosa Rademakers Bioinformatics, Volume 39, Issue 5, May 2023, btad311, doi
External guides and resources¶
- If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za