malab/cafu repository overview

RNA-Seq is a powerful tool to study transcriptome characteristics in both model and non-model species. The RNA-Seq data is generally analyzed by aligning short reads to genome sequences. Usually unmapped RNA-Seq reads are discarded from the analysis process, resulting to a loss of significant biological information and insights.

CAFU is a Galaxy-based bioinformatics framework for comprehensive assembly and functional annotation of unmapped RNA-seq data from single- and mixed-species samples which integrates plenty of existing NGS analytical tools and our developed programs, and features an easy-to-use interface to manage, manipulate and most importantly, explore large-scale unmapped reads.

Besides the common process of reads cleansing, reads mapping, unmapped reads generation and novel transcription assembly, CAFU optionally offers the multiple-level evidence analysis of assembled transcripts, the sequence and expression characteristics of assembled transcripts, and the functional exploration of assembled transcripts through gene co-expression analysis and genome-wide association analysis.

Taking the advantages of machine learning (ML) technologies, CAFU also effectively addresses the challenge of classifying species-specific transcript assembled using unmapped reads from mixed-species samples.

The CAFU project is hosted on GitHub(https://github.com/cma2015/CAFU⁠) and can be accessed from http://bioinfo.nwafu.edu.cn:4001⁠. The CAFU Docker image is available at https://hub.docker.com/r/malab/cafu⁠.

CAFU is developed and maintained by the lab of Prof. Chuang Ma at the center of Bioinformatics, College of Life Sciences, Northwest A&F University. For comments/suggestions/error reports, please contact Siyuan Chen ([email protected]⁠) or Jingjing Zhai ([email protected]⁠)