{"repo":"nf-core/riboseq","free":true,"listed":false,"github":"https://github.com/nf-core/riboseq","clone":"git clone https://github.com/nf-core/riboseq.git","description":"Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.","language":"Nextflow","stars":35,"topics":["nextflow","nf-core","pipeline","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/riboseq is a bioinformatics pipeline for analysis of Ribo-seq data. It borrows heavily from nf-core/rnaseq in the preprocessing stages: 1. Merge re-sequenced FastQ files ( cat ) 2. Sub-sample FastQ files and auto-infer strandedness ( fq , Salmon ) 3. Read QC ( FastQC ) 4. UMI extraction ( UMI-tools ) 5. Adapter and quality trimming ( Trim Galore! ) 6. Removal of genome contaminants ( BBSplit ) 7. Removal of ribosomal RNA ( SortMeRNA ) 8. Genome alignment of reads, outputting both genome and transcriptome alignments with STAR 9. Sort and index alignments ( SAMtools ) 10. UMI-based deduplication ( UMI-tools ) Differences occur in the downstream analysis steps. Currently these specialist steps are: 1. Check reads distribution around annotated protein coding regions on user provided transcripts, show frame bias and estimate P-site offset for different group of reads ( Ribo-TISH ) 2. (default, optional) Predict translated open reading frames and/ or translation initiation sites de novo from alignment data ( Ribo-TISH ) 3. (default, optional) Derive candidate ORFs from reference data and detect translated ORFs from that list ( Ribotricer ) 4. (default, optional) Derive P-sites and QC from transcriptome alignments ( riboWaltz ) 5. (optional) Use a translational efficiency approach to study the dynamics of transcription and translation, with anota2seq. requires matched RNA-seq and Ribo-seq data Usage [!NOTE] If you are new to Nextflow and nf-core, please refer to","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/riboseq/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}