reorient-circular-seq

reorient-circular-seq is a tool designed to reorient circular DNA sequences to prevent the truncation of genes that span the sequence's endpoints. Here's a concise overview of its process:

1. Gene prediction: pyrodigal-gv is used to predict genes within the circular DNA sequence.
2. Assessment of truncated genes: The tool checks if the first and/or last predicted genes are split by the current linear breakpoint.
3. Shift breakpoint: Rotates the sequence to move the breakpoint to the center of the longest intergenic (between two CDSs) region.
4. Iterate if necessary: The gene prediction is run again on the reoriented sequence. If truncated genes are still exist, the breakpoint is shifted to the next longest intergenic region. This process repeats until a configuration with no truncated genes is found or all intergenic regions have been tried.

By systematically adjusting the breakpoint to optimal intergenic areas, reorient-circular-seq tries to increase the amount of genes are fully intact in the linear representation.

Installation

$ git clone https://github.com/apcamargo/reorient-circular-seq.git
$ cd reorient-circular-seq
$ pixi run reorient-circular-seq -h

Usage

$ reorient-circular-seq [OPTIONS] [INPUT] [OUTPUT]

Positional arguments

Argument	Description
input	Input FASTA file (default: stdin)
output	Output FASTA file (default: stdout)

Options

Option	Short	Value type	Description	Default
--remove-tr			Trim terminal repeats from the ends of the sequences.
--min-tr-length		Integer (≥1)	Minimum length of the terminal repeat to be removed. Only used if --remove-tr is set.	21
--threads	-t	Integer (1–16)	Number of threads to use.	4
--verbose	-v	Integer (0–2)	Verbosity level.	0
--help	-h		Show this message and exit.