ONT / TnSeq

TnSeq_ONT

Anchor-based flank extraction and clustering for ONT amplicon/TnSeq-style analysis.

STATUS: TEST IN PROGRESS

Pipeline Flow

Read Scan→ Anchor Match→ Flank Extraction→ Clustering→ Summary Output

Run

python TnSeq_ONT/Go_search_tnseq_flank.py --help

Real Example

python TnSeq_ONT/Go_search_tnseq_flank.py \
  --input TnSeq_ONT/20261101_TNSEQ_HKP/reads.fastq.gz \
  --anchor Tn_anchor.fa \
  --outdir TnSeq_ONT/20261101_TNSEQ_HKP_out

Purpose

Use this workflow to extract transposon flanks from ONT reads and cluster insertion-related signals.

Options

FlagDescription
--inputInput read file
--anchorAnchor sequence file
--outdirOutput directory

Expected Input

TnSeq_ONT/
|-- 20251101_TNSEQ_HKP/
|-- 20251101_TNSEQ_HKP_out/
|-- 20261101_TNSEQ_HKP/
|   `-- reads.fastq.gz
`-- 20261101_TNSEQ_HKP_out/

TnSeq_ref/
`-- Tn_anchor.fa

Main Outputs

TnSeq_ONT/
|-- 20251101_TNSEQ_HKP/
|-- 20251101_TNSEQ_HKP_out/
|-- 20261101_TNSEQ_HKP/
`-- 20261101_TNSEQ_HKP_out/
    |-- extracted_flanks/
    |-- clustered_flanks/
    `-- flank_summary.tsv