ECuADOR

ECuADOR automates post-processing of assembled plastomes from NGS, Sanger sequencing, or assembler outputs by detecting inverted repeat regions and reorganizing chloroplast sequences into a standardized LSC-Irb-SSC-IRa order for alignment and phylogenetic analyses.

Key Features:

• Perl implementation: The software is implemented as a Perl script that automates detection and reorganization of plastome sequences.
• Sliding-window repeat detection: A sliding-window approach identifies long repeated sequences to enable precise identification of inverted repeat regions (IRs).
• Robust IR identification: IR detection tolerates artifactual breaks and sequencing errors in draft sequences.
• Sequence reordering: Reorganizes plastome sequences into the LSC-Irb-SSC-IRa order to produce ready-to-align chloroplast genomes.
• Variable region and SNP support: Facilitates detection of variable regions within chloroplast genomes and supports single nucleotide polymorphism (SNP) analysis.
• Performance and testing: Validated on 161 chloroplast datasets across angiosperm phylogeny with reported accuracy >99%, runtime under 20 minutes, and peak memory usage up to 150 MB.
• De novo recognition and re-ordination: Performs de novo recognition and re-ordination of plastomes in a single processing step.

Scientific Applications:

• Phylogenetic reconstruction: Produces standardized plastome sequences suitable for phylogenetic reconstruction at various taxonomic levels.
• Comparative genomics: Enables generation of genome alignments for comparative genomic studies of chloroplast DNA.
• Phylogenomics and SNP-based analyses: Supports identification of variable regions and SNPs for phylogenomic and population-level analyses.

Methodology:

Perl script uses a sliding-window approach to detect long repeats and inverted repeat regions (IRs), tolerates artifactual breaks and sequencing errors, and reorganizes sequences into LSC-Irb-SSC-IRa order from inputs originating from NGS, Sanger sequencing, or assembler outputs.