TraDIS-ONTA set of Python scripts for processing Oxford Nanopore sequencing reads from Transposon-Directed Insertion Site Sequencing (TraDIS) experiments.Versions

v28d014d (default)

Tags: nanopore, TraDIS, transposon, genomicsParameters

reads (file) required: Input ONT reads in FASTQ format.

start (file) required: FASTA file containing the transposon start sequence.

end (file): FASTA file containing the transposon end sequence.

reference (file) required: Reference genome in FASTA format for alignment.

min_id (int): Minimum alignment percent identity for start/end sequences (default: 95).

max_gap (int): Maximum allowed gap in bp for start/end sequences (default: 5).

neg_id (int): Minimum alignment percent identity for negative sequences (default: 95).

neg_gap (int): Maximum allowed gap in bp for negative sequences (default: 5).

trim (int): Trim output reads so they do not exceed this length (default: do not trim to a target length).

Links

Home page

GitHub repository

License: GPL-3.0

Open TraDIS-ONT in the CPG Portal. Configuring and running a tool needs JavaScript.