pELF-FinderpELF-Finder screens paired-end Illumina FASTQ reads from Enterococcus isolates for pELF-like linear plasmid terminal markers. It maps reads against conserved pELF1 left- and right-terminal reference sequences using Bowtie2 and computes mapped-read counts, reference breadth, and mean depth using Samtools. Samples are classified as pELF-positive when both terminal markers meet the minimum mapped-read threshold.Versions

v0.1.0 (default)

Tags: bioinformatics, plasmid detection, Enterococcus, linear plasmids, whole genome sequencing, paired-end sequencing, Bowtie2Parameters

reads_r1 (file, multiple) required: Forward (R1) FASTQ reads, ordered to match reads_r2.

reads_r2 (file, multiple) required: Reverse (R2) FASTQ reads in the same sample order as reads_r1. Both lists must have equal length.

min_reads (int): Minimum mapped reads at each terminal marker for a pELF-positive classification.

Links

License: GPL-3.0

Cite as: pELF-Finder v0.1.0. Marwa Alhothali. GitHub: https://github.com/Marwa-Alhothali/pELF-Finder. Associated preprint: https://doi.org/10.64898/2026.05.08.26352429.

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