{"repo":"nf-core/phageannotator","free":true,"listed":false,"github":"https://github.com/nf-core/phageannotator","clone":"git clone https://github.com/nf-core/phageannotator.git","description":"Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.","language":"Nextflow","stars":19,"topics":["nextflow","nf-core","pipeline","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/phageannotator is a bioinformatics pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences. Pipeline summary The core identification/quantification portion of this pipeline takes (meta)-genomic assemblies (as output by nf-core/mag ) and performs the following steps: 1. Phage sequence identification - de novo identification ( geNomad ) - OPTIONAL - reference-based identification ( mash ) 2. Quality assessment/filtering ( CheckV ) 3. ANI clustering/dereplication ( BLAST )( CheckV ) 4. Binning ( VRhyme ) 5. Abundance estimation ( bowtie2 )( CoverM ) - Output can be used as input for nf-core/differentialabundance 6. OPTIONAL - Strain profiling ( inStrain ) 7. OPTIONAL - Prophage activity prediction ( propagAtE ) The annotation portion of this pipeline performs the following steps: 1. Marker-based taxonomic classification ( geNomad ) 2. Genome proximity taxonomic classification ( mash ) 3. Host prediction ( iPHoP ) 4. Lifestyle prediction ( BACPHLIP ) 5. Protein-coding gene prediction ( Prodigal-gv ) - Output can be used as input for nf-core/funcscan Quick Start 1. Install Nextflow ( =22.10.1 ). 2. Install any of Docker , Singularity (you can follow this tutorial), Podman , Shifter or Charliecloud for full pipeline reproducibility (you can use Conda both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see docs) . 3. Download the pipeline and","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/phageannotator/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."}