NAME¶

dnachisel - optimize DNA sequences under constraints

SYNOPSIS¶

dnachisel source target [--circular] [--mute] [--with_sequence_edits]

DESCRIPTION¶

DNA Chisel optimizes a DNA sequence according to constraints and optimization objectives annotated in a GenBank record. source is a FASTA or GenBank file. GenBank feature labels beginning with @ define constraints; labels beginning with ~ define optimization objectives.

If target ends in .gb, the optimized sequence is written as a GenBank file. Otherwise it names a directory or a ZIP archive ending in .zip, and a complete optimization report is generated. Report generation requires the optional Python reporting libraries.

OPTIONS¶

--circular

Treat the input sequence as circular DNA.

--mute

Suppress progress messages.

--with_sequence_edits

Annotate sequence edits when writing a GenBank output file.

-h, --help

Show usage information.

EXAMPLE¶

dnachisel annotated_record.gb optimized_record.gb

SEE ALSO¶

The HTML manual is provided by the python-dnachisel-doc package.

https://edinburgh-genome-foundry.github.io/DnaChisel/