integrativebioinformatics/longnoncoder is a bioinformatics nextflow pipeline that provides a comprehensive analysis of raw long-read RNA-seq data, encompassing transcriptome assembly, quantification, and characterization. The pipeline reports a detailed overview on the entire transcriptome with particular emphasis on lncRNA structure and isoforms across annotated transcripts and novel candidates.
For more details and further functionality, please refer to the usage and output documentations.
Important
LongNonCoder is compatible Ensembl reference genomes and annotations from the following organisms: > Homo sapiens, Mus musculus, Danio rerio, Anolis carolinensis, Chrysemys picta belli, Eptatetrus burgeri, Gallus gallus, Latimeria chalumnae, Monodelphis domestica, Notechis scutatus, Ornithorhynchus anatinus, Petromyzon marinus, Sphenodon punctatus, and Xenopus tropicalis. In the next releases, we plan to update the pipeline workflow to cover more organisms or even more general taxonomic classes.
We can describe each step of the workflow as follows:
- Quality control of reads (NanoComp)
- Filtering and trimming (chopper)
- Mapping to a genome reference (minimap2 and samtools)
- Quality control of mapped reads (NanoComp)
- Transcriptome Assembly (Bambu)
- Compare novel transcripts to the annotation reference (GffCompare)
- Convert novel transcripts
GTFfile toFASTA(GffRead) - Predict transcripts as protein-coding or non-coding (RNAmining)
- Gather all data from previous steps and generate informative and re-usable metadata
.csvandGTFfiles for both novel and annotated transcripts (Metadata handling) - Provide a report and data visualization for the full transcriptome, with emphasis on lncRNAs (Report)
- Gather all possible QC information from the previous steps (MultiQC)
Note
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. The pipeline is compatible with Docker and Singularity/Apptainer.
You can run an example test by following the instructions:
Enter the test_data folder
cd test_dataDownload and unzip the reference FASTA and GTF files, and also download the fastq.gz files:
Make the file executable!!
chmod +x download-ref-fastq.shRun it
./download-ref-fastq.shAdd YOUR full path for the samples in the samplesheet.csv (file). For example, your full path for a sample could be:
home/user/longnoncoder/test_data/thesample.fastq.gz
Go back to the main directory and execute the test!
cd ..nextflow run main.nf -profile test,singularity -params-file test_data/testing.ymlWarning
Please provide pipeline parameters via the CLI or Nextflow -params-file option and input a yaml parameters file. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.
If you would like to contribute to this pipeline, please see the contributing guidelines.
If you use integrativebioinformatics/longnoncoder in your research, please consider citing it.
An extensive list of references for the tools incorporated by the pipeline can be found in the CITATIONS.md file.
The longnoncoder pipeline was originally developed by Bárbara Borges (@borgessbarbara). We extend our sincere thanks to Lucas Freitas (@lfreitasl), João Cavalcante (@jvfe), and Gleison Azevedo (@gleisonm for their significant contributions and assistance.
This project was carried out under the leadership and supervision of Principal Investigators Vinícius Maracajá-Coutinho, Thaís Gaudencio, and Rodrigo Dalmolin.
This project was supported by the High-Performance Computing Center at UFRN (NPAD/UFRN) and the National Laboratory for High Performance Computing (NLHPC) (CCSS210001) at UChile.
CAPES (001), CNPq (MCTI/FNDCT 445067/2024-1), FONDECYT-ANID Postdoctorado (3250452), FONDECYT-ANID (1211731), FONDAP-ANID (15130011 and 1523A0008), and Anillo-ANID (ATE220016).
