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GARM

Genome Assembly, Reconciliation and Merging

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Short read assemblers and mappers

General Information

img GARM is (Genome Assembler, Reconcilation and Merging) a new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies. It relies on the observation that a combination of sequencing methods will work better together to reconstruct a genome in its totality, overcoming the limitations of each technology and assembly method if they were used in isolation. The pipeline is based on perl scripts and third-party open source software like the AMOS package. The method merges contigs and scaffolds from different assemblers using the same or different sequencing technologies. When scaffolds are provided, a process for finding compressions and extensions (CE) problems in the genome can be performed; scaffolds can also be reconstructed recalculating the gaps between contigs. It has been tested with three major sequencing technologies (Sanger, 454 and Illumina) using real sequencing data for some organisms where a reference genome is available or where a manual post-assembly process of improvement is being undertaken at the Wellcome Trust Sanger Institute.

Description

The pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on Debian, Ubuntu, Fedora and BioLinux distributions. The method merges contigs or scaffolds from different assemblers using the same or different sequencing technologies. When scaffolds are provided, a process of finding probable compressions or extensions (CE) problems in the assemblies can be per-formed; contigs are joined back into scaffolds after gap recalculation

Requirements

  • Perl v5.8 or above
  • Perl modules: Parallel::ForkManager, List::MoreUtils
  • AMOS (tested on v3.0.0)
  • MUMmer (tested on v3.22)
  • R language(for GC plots only)

Please, make sure that everything is installed and running properly