aTRAM

aTRAM (automated Target Restricted Assembly Method) is a software tool that enables rapid assembly of genes from next-generation sequencing data, even for taxa that lack a closely related reference genome. Traditional de novo genome assembly approaches can be time-consuming and computationally intensive, often requiring days of processing time and various genomic libraries. aTRAM addresses these challenges using a targeted approach to assemble genes of interest quickly and efficiently.

Key features and benefits of aTRAM:

1. Utilizes a reference sequence, BLAST, and an iterative approach to target and locally assemble specific genes.

2. Rapidly assembles genes across distantly related taxa without needing a closely related reference genome.

3. Significantly reduces the time required for gene assembly, taking on average less than 1 minute per gene in comparative tests with closely related taxa.

4. Demonstrates high gene recovery rates (97-99%) when tested on taxa ranging from 25 to 110 million years divergent from the reference taxon.

5. Eliminates the need for draft genome assembly of all taxa of interest, saving time and computational resources.

6. Particularly useful for phylogenomic projects covering a wide taxonomic range, as it can quickly assemble genes across distantly related taxa.

Topic

Sequence assembly;Sequencing

Detail

  • Operation: Sequence assembly

  • Software interface: Command-line interface

  • Language: Python

  • License: BSD 3-Clause "New" or "Revised" License

  • Cost: Free of charge with restrictions

  • Version name: v2.4.3

  • Credit: The National Science Foundation, Genome Canada, Natural Sciences and Engineering Research Council of Canada.

  • Input: -

  • Output: -

  • Contact: Julie M Allen juliema@illinois.edu

  • Collection: -

  • Maturity: Stable

Publications

  • aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data.
  • Allen JM, et al. aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data. aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data. 2015; 16:98. doi: 10.1186/s12859-015-0515-2
  • https://doi.org/10.1186/s12859-015-0515-2
  • PMID: 25887972
  • PMC: PMC4380108

Download and documentation


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