Ag Data Commons
10 files

Data from polishCLR: Example input genome assemblies

posted on 2024-02-13, 15:33 authored by Amanda R. Stahlke, Brad S. Coates

[ NOTE - Data files added 2022-11-01:

  • Test long reads - test.1.filtered.bam_.gz
  • Test short reads R1 - testpolish_R1.fastq
  • Test short reads R2 - testpolish_R2.fastq
  • Chromosome 30 of H. zea - GCF_022581195.2_ilHelZeax1.1_chr30.fasta ]

In order to produce the best possible de novo, chromosome-scale genome assembly from error prone Pacific BioSciences continuous long reads (CLR) reads, we developed a publicly available, flexible and reproducible workflow that is containerized so it can be run on any conventional HPC, called polishCLR. This dataset provides example input primary contig assemblies to test and reproduce the demonstrated utility of our workflow.

The polishCLR workflow can be easily initiated from three input cases: Case 1: An unresolved primary assembly with associated contigs, the output of FALCON 2-asm: p_ctg.fasta and a_ctg.fasta Case 2: A haplotype-resolved but unpolished set, the output of FALCON-Unzip 3-unzip: all_p_ctg.fasta and all_h_ctg.fasta Case 3: A haplotype-resolved, CLR long-read, Arrow-polished set of primary and alternate contigs, the output of FALCON-Unzip 4-polish: cns_p_ctg.fasta and cns_h_ctg.fasta.

These example data are the input contigs assemblies for the pest Helicoverpa zea. These contigs are built from 49.89 Gb of raw Pacific Biosciences (PacBio) CLR data generated from a single H. zea HzStark_Cry1AcR strain male.

Adult H. zea were collected near the USDA-ARS Genetics and Sustainability Agricultural Research Unit, Starkville, MS, USA in 2011, and transported to and maintained in a colony at the USDA Southern Insect Management Unit (SIMRU), Stoneville, MS, USA as described previously. Larvae were selected on a diagnostic dose of 2.0 μg ml-1 purified Cry1Ac, and survivors used to create the strain, HzStark_Cry1AcR. HzStark_Cry1AcR was back-crossed every 5 generations to a susceptible line maintained at USDA-ARS SIMRU.

A single male pupa (homogametic, ZZ sex chromosome) from HzStark_Cry1AcR was dissected laterally into eight ~20 μg sections. High molecular weight DNA was extracted. PacBio libraries were generated from unsheared DNA using a SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences, Menlo Park, CA, USA), and 20 hour run time movies generated on a single SMRT Cell 1M v3 using the Sequel I system (Pacific Biosciences).

The raw continuous long read (CLR) subread bam files were converted to fastq format using bamtools v. 2.5.1 (Barnett et al. 2011), then used as input for the Falcon assembler (Chin et al. 2016) using the pb-assembly conda environment v. (Pacific Biosciences; default parameters). Falcon-Unzip created primary and alternate contigs with one round of haplotype-aware polishing by Arrow (Pacific Biosciences).

Resources in this dataset:

  • Resource Title: Associated assembly contigs output from FALCON/2-asm-falcon.

    File Name: a_ctg_all.fasta

  • Resource Title: Primary assembly contigs output from FALCON/2-asm-falcon.

    File Name: p_ctg.fasta

  • Resource Title: Alternate haplotype assembly contigs output from FALCON Unzip 3-unzip.

    File Name: all_h_ctg.fasta

  • Resource Title: Primary assembly contigs output from FALCON Unzip 3-unzip.

    File Name: all_p_ctg.fasta

  • Resource Title: Alternate assembly contigs output from FALCON Unzip 4-polish.

    File Name: cns_h_ctg.fasta

  • Resource Title: Primary assembly contigs output from FALCON Unzip 4-polish.

    File Name: cns_pctg.fasta

  • Resource Title: Test long reads.

    File Name: test.1.filtered.bam.gz

    Resource Description: For testing the pipeline, long reads that map to H. zea chromosome 30

  • Resource Title: Test short reads R1.

    File Name: testpolish_R1.fastq

    Resource Description: Short reads aligned to Chromosome 30 of H. zea

  • Resource Title: Test short reads R2.

    File Name: testpolish_R2.fastq

    Resource Description: Reverse pair (R2) short reads aligned to Chromosome 30 of H. zea

  • Resource Title: Chromosome 30 of H. zea.

    File Name: GCF_022581195.2_ilHelZeax1.1_chr30.fasta


USDA-ARS: 5030-22000-019-00-D

USDA-ARS: 0500-00093-001-00-D


Data contact name

Stahlke, Amanda

Data contact email


Ag Data Commons

Intended use

These data should be used to test the polishCLR workflow.

Temporal Extent Start Date



  • notPlanned


  • Not specified

Geographic Coverage


Geographic location - description

Starkville, MS, USA

ISO Topic Category

  • biota
  • farming

National Agricultural Library Thesaurus terms

genome assembly; Helicoverpa zea; DNA; genetic techniques and protocols; Biological Sciences

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 304
  • 305

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Stahlke, Amanda R.; Coates, Brad S. (2022). Data from polishCLR: Example input genome assemblies. Ag Data Commons.

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