{"repo":"nf-core/metatdenovo","free":true,"listed":false,"github":"https://github.com/nf-core/metatdenovo","clone":"git clone https://github.com/nf-core/metatdenovo.git","description":"Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.","language":"Nextflow","stars":35,"topics":["nf-core","nextflow","pipeline","workflow","eukaryotes","metagenomics","metatranscriptomics","prokaryotes","viruses"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/metatdenovo is a bioinformatics best-practice analysis pipeline for assembly and annotation of metatranscriptomic and metagenomic data from prokaryotes, eukaryotes or viruses. On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website. Usage 1. Read QC ( FastQC ) 2. Present QC for raw reads ( MultiQC ) 3. Quality trimming and adapter removal for raw reads ( Trim Galore! ) 4. Optional: Filter sequences with BBduk 5. Optional: Normalize the sequencing depth with BBnorm 6. Merge trimmed, pair-end reads ( Seqtk ) 7. Choice of de novo assembly programs: 1. RNAspades suggested for both prokaryote and eukaryote assembly 2. Megahit suggested for both prokaryote and eukaryote assembly; requires less resources 8. Choice of orf caller: 1. TransDecoder suggested for eukaryotes; only ORFs 2. Prokka suggested for prokaryotes; ORFs and other features plus functional annotation 3. Prodigal suggested for Prokaryotes; only ORFs 9. Quantification of genes identified in assemblies: 1. Generate index of assembly ( BBmap index ) 2. Mapping cleaned reads to the assembly for quantification ( BBmap ) 3. ","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/metatdenovo/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."}