{"repo":"nf-core/genomeassembler","free":true,"listed":false,"github":"https://github.com/nf-core/genomeassembler","clone":"git clone https://github.com/nf-core/genomeassembler.git","description":"Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads","language":"Nextflow","stars":34,"topics":["nf-core","nextflow","workflow","pipeline","genome-assembly"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/genomeassembler is a bioinformatics pipeline that carries out genome assembly, polishing and scaffolding from long reads (ONT or pacbio). Assembly can be done via flye or hifiasm , polishing can be carried out with medaka (ONT), or pilon (requires short-reads), and scaffolding can be done using LINKS , Longstitch , or RagTag (if a reference is available). Quality control includes BUSCO , QUAST and merqury (requires short-reads). Currently, this pipeline does not implement phasing of polyploid genomes or HiC scaffolding. Usage [!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data. First, prepare a samplesheet with your input data that looks as follows: samplesheet.csv : Each row represents one genome to be assembled. sample should contain the name of the sample, ontreads should contain a path to ONT reads (fastq.gz), hifireads a path to HiFi reads (fastq.gz), ref fasta and ref gff contain reference genome fasta and annotations. shortread F and shortread R contain paths to short-read data, paired indicates if short-reads are paired. Columns can be omitted if they contain no data, with the exception of shortread R , which needs to be present if shortread F is there, even if it is empty. Now, you can run the pipeline using: [!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom con","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/genomeassembler/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."}