<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36478?offset=560 https://bioinformaticsonline.com/bookmarks/view/44768/tritex-a-computational-pipeline-for-chromosome-scale-assembly-of-plant-genomes Fri, 14 Feb 2025 10:53:48 -0600 https://bioinformaticsonline.com/bookmarks/view/44768/tritex-a-computational-pipeline-for-chromosome-scale-assembly-of-plant-genomes <![CDATA[TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes]]> This is the documentation of TRITEX, a computational pipeline for chromosome-scale assembly of plant genomes. It was developed in the research group Domestication Genomics at the Leibniz Institute of Plant Genetics and Crop Research (IPK) Gatersleben.

Address of the bookmark: https://tritexassembly.bitbucket.io/

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/26332/pilon Mon, 08 Feb 2016 15:56:18 -0600 https://bioinformaticsonline.com/bookmarks/view/26332/pilon <![CDATA[Pilon]]> Pilon is a software tool which can be used to:

  • Automatically improve draft assemblies
  • Find variation among strains, including large event detection

Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

  • Single base differences
  • Small indels
  • Larger indel or block substitution events
  • Gap filling
  • Identification of local misassemblies, including optional opening of new gaps

More at https://github.com/broadinstitute/pilon/wiki

Address of the bookmark: https://github.com/broadinstitute/pilon/wiki

]]> Rahul Nayak