Automatic Basic Preprocessing

Automatic Basic Preprocessing#

automatic_script.py is a command-line driver that runs the standard verkko-fillet preprocessing and QC pipeline end-to-end on a finished Verkko assembly. It is intended for users who do not want to step through the notebook tutorials interactively and just want the figures, stats, and chromosome-assignment files generated in one go.

The script is shipped with the package at:

verkko-fillet/src/verkkofillet/bin/automatic_script.py

What it does#

Given a Verkko output directory, a reference FASTA, and a chromosome name mapping file, the script:

  1. Loads the Verkko assembly into a VerkkoFillet object (vf.pp.read_Verkko)

  2. Detects T2T contigs (vf.tl.getT2T)

  3. Assigns reference chromosomes via mashmap (vf.tl.chrAssign)

  4. Reads the chromosome mapping (vf.pp.readChr)

  5. Detects broken contigs (vf.pp.detectBrokenContigs)

  6. Generates QC plots:

    • vf.pl.showMashmapOri — chromosome coverage from mashmap

    • vf.pl.completePlot — completeness per chromosome/haplotype

    • vf.pl.contigLenPlot — contig length per haplotype

    • vf.pl.contigPlot — T2T status heatmap

    • vf.pl.n50Plot — N50 line plot

  7. Detects internal telomeres and computes telomere percentages (vf.tl.detect_internal_telomere, vf.pp.find_intra_telo, vf.pl.percTel)

All outputs are written under the Verkko-fillet working directory (obj.verkko_fillet_dir):

Output

Location

Figures (PDF)

<verkko_fillet_dir>/figs/

Stats tables

<verkko_fillet_dir>/stats/

Chromosome assignment files

<verkko_fillet_dir>/chromosome_assignment/

Requirements#

  • verkkofillet installed (and importable as verkkofillet)

  • External tools used by the underlying functions: mashmap, samtools, bgzip, seqtk (as required by chrAssign / FASTA renaming)

  • A completed Verkko assembly directory

Arguments#

Argument

Required

Default

Description

--verkkoDir

yes

—

Path to the Verkko output directory.

--ref

yes

—

Reference FASTA file used for chromosome assignment.

--map_file

yes

—

Tab-separated mapping from contig names in the reference FASTA to the desired chromosome names.

--internal_tel_threshold

no

15000

Distance from contig end (bp) used to flag internal telomeres.

--map_file format#

A two-column, tab-separated file:

<contig_name_in_fasta>\t<desired_chromosome_name>

Examples:

# contig is already named as desired
chr1        chr1
chr2        chr2     


# rename contig GCF00001 to chr1
GCF00001    chr1        
GCF00002    chr2

Usage#

python /path/to/verkko-fillet/src/verkkofillet/bin/automatic_script.py \
    --verkkoDir /path/to/verkko_output \
    --ref       /path/to/reference.fasta \
    --map_file  /path/to/chrMap.tsv \
    --internal_tel_threshold 15000

Example#

python automatic_script.py \
    --verkkoDir ./verkko_asm \
    --ref       ./ref/CHM13v2.fa \
    --map_file  ./ref/chrMap.tsv

After the run completes, inspect the results: The final verkko-fillet output directory is created next to the input Verkko directory and named {verkko_directory}_verkko_fillet.

ls verkko_asm_verkko_fillet/figs/
ls verkko_asm_verkko_fillet/stats/
ls verkko_asm_verkko_fillet/chromosome_assignment/
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