{"repo":"nf-core/rnaseq","free":true,"listed":false,"github":"https://github.com/nf-core/rnaseq","clone":"git clone https://github.com/nf-core/rnaseq.git","description":"RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.","language":"Nextflow","stars":1350,"topics":["nf-core","nextflow","workflow","rna-seq","rna","pipeline"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/rnaseq is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet with FASTQ files or pre-aligned BAM files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report. In case the image above is not loading, please have a look at the static version. 1. Merge re-sequenced FastQ files ( cat ) 2. Auto-infer strandedness by subsampling and pseudoalignment ( 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. Choice of multiple alignment and quantification routes ( For STAR the sentieon implementation can be chosen ): 1. STAR - Salmon 2. STAR - RSEM 3. HiSAT2 - NO QUANTIFICATION 9. Sort and index alignments ( SAMtools ) 10. UMI-based deduplication ( UMI-tools ) 11. Duplicate read marking ( picard MarkDuplicates ) 12. Transcript assembly and quantification ( StringTie ) 13. Create bigWig coverage files ( BEDTools , bedGraphToBigWig ) 14. Extensive quality control: 1. RSeQC 2. Qualimap 3. dupRadar 4. Preseq 5. DESeq2 6. Contamination detection on selected screening reads (unaligned by default); optional 1. Kraken2 - Bracken 2. Sylph 15. Pseudoalignment and quantification ( Salmon or 'Kallisto'; optional ) 16. Present QC for raw re","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/rnaseq/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."}