{"repo":"nf-core/denovotranscript","free":true,"listed":false,"github":"https://github.com/nf-core/denovotranscript","clone":"git clone https://github.com/nf-core/denovotranscript.git","description":"A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq","language":"Nextflow","stars":26,"topics":["denovo-assembly","rna-seq","transcriptome","nextflow","nf-core","pipeline","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/denovotranscript is a bioinformatics pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq. It takes a samplesheet and FASTQ files as input, perfoms quality control (QC), trimming, assembly, redundancy reduction, pseudoalignment, and quantification. It outputs a transcriptome assembly FASTA file, a transcript abundance TSV file, and a MultiQC report with assembly quality and read QC metrics. 1. Read QC of raw reads ( FastQC ) 2. Adapter and quality trimming ( fastp ) 3. Read QC of trimmed reads ( FastQC ) 4. Remove rRNA or mitochondrial DNA (optional) ( SortMeRNA ) 5. Transcriptome assembly using any combination of the following: - Trinity with normalised reads (default=True) - Trinity with non-normalised reads - rnaSPAdes medium filtered transcripts outputted (default=True) - rnaSPAdes soft filtered transcripts outputted - rnaSPAdes hard filtered transcripts outputted 6. Redundancy reduction with Evidential Gene tr2aacds . A transcript to gene mapping is produced from Evidential Gene's outputs using gawk . 7. Assembly completeness QC ( BUSCO ) 8. Other assembly quality metrics ( rnaQUAST ) 9. Transcriptome quality assessment with TransRate , including the use of reads for assembly evaluation. This step is not performed if profile is set to conda or mamba . 10. Pseudo-alignment and quantification ( Salmon ) 11. HTML report for raw reads, trimmed reads, BUSCO, and Salmon ( MultiQC ) Usage [!NOTE] If you are new to Nextflow","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/denovotranscript/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."}