View the READ THE DOCs (RTD) Manual for PolishCLR. This RTD manual contains step by step instructions and test datasets on how to use PolishCLR.
polishCLR is a nextflow workflow for polishing genome assemblies (improving accuracy) generated with noisy PacBio reads using accurate, short Illumina reads. It implements the best practices described by the Vertebrate Genome Project (VGP) Assembly community (Rhie et al. 2021) and extends these for use-cases we found common in the Ag100Pest Genome Initiative. This workflow was developed as part of the USDA-ARS Ag100Pest Initiative. The authors thank members of the USDA-ARS Ag100Pest Team and SCINet Virtual Resource Support Core (VRSC) for fruitful discussions and troubleshooting throughout the development of this 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) or without (e.g., the output of Canu or wtdbg2).
- Case 2: A haplotype-resolved but unpolished set (e.g., the output of FALCON-Unzip 3-unzip).
- Case 3: IDEAL! A haplotype-resolved, CLR long-read, Arrow-polished set of primary and alternate contigs (e.g., the output of FALCON-Unzip 4-polish).
We strongly recommend including the organellular genome to improve the polishing of nuclear mitochondrial or plasmid pseudogenes (Howe et al., 2021). Organelle genomes should be generated and polished separately for best results. You could use the mitochondrial companion to polishCLR, polishCLRmt or mitoVGP (Formenti et al., 2021).
To allow for the inclusion of scaffolding before final polishing and increase the potential for gap-filling across correctly oriented scaffolded contigs, the core workflow is divided into two steps, controlled by a --step parameter flag.
You can view a more complete visualization of the pipeline in Supp. Fig. S1
You can find more details on the usage below. These also include a simple basic run to run the analyses on your own genomes.
This pipeline will require nextflow. The rest of the dependencies can be installed via miniconda, Docker, or Singularity
nextflow -version
nextflow run isugifNF/polishCLR -r main \
--help
For ag100pest projects, we have been installing dependencies in a miniconda environment. Dependencies may also be installed via docker or singularity.
To update to the latest version of the pipeline, run:
nextflow pull isugifNF/polishCLR -r main
Install dependencies in a miniconda environment.
wget https://raw.githubusercontent.com/isugifNF/polishCLR/main/other_dependencies.yml
[[ -d env ]] || mkdir env
conda env create -f other_dependencies.yml -p ${PWD}/env/polishCLR_env
conda activate env/polishCLR_env
nextflow run isugifNF/polishCLR -r main \
--check_software
NOTE
if you run into the error ERROR: Unable to load secrets provider while running the nextflow command
Then define NXF_HOME where your nextflow script is located.
For example:
export NXF_HOME=~/.conda/envs/nextflow/bin
Your nextflow location may differ. Use which nextflow to locate the path to your nextflow you have installed.
Start up docker and pull the csiva2022/polishclr:latest image.
docker pull csiva2022/polishclr:latest
# Option 1
docker run -it csiva2022/polishclr:latest \
nextflow run isugifNF/polishCLR -r main \
--check_software
# Option 2
nextflow run isugifNF/polishCLR -r main \
--check_software \
-profile docker
# Option 3
nextflow run isugifNF/polishCLR -r main \
--check_software \
--with-docker csiva2022/polishclr:latest
Run the polishCLR pipeline with an added -with-docker csiva2022/polishclr:latest parameter. See nextflow docker run documentation for more information.
Install dependencies as a singularity image.
singularity pull polishclr.sif docker://csiva2022/polishclr:latest
# Option 1:
singularity exec polishclr.sif \
nextflow run isugifNF/polishCLR -r main \
--check_software
# Option 2:
nextflow run isugifNF/polishCLR -r main \
--check_software \
-profile singularity
# Option 3:
nextflow run isugifNF/polishCLR -r main \
--check_software \
-with-singularity polishclr.sif
Run the polishCLR pipeline with an added -with-singularity polishclr.sif parameter. See nextflow singularity run documentation for more information.
Print usage statement
nextflow run isugifNF/polishCLR -r main --help
N E X T F L O W ~ version 21.04.2
Launching `main.nf` [lonely_liskov] - revision: 6a81970115
----------------------------------------------------
\\---------//
___ ___ _ ___ ___ \\-----//
| (___ | | / _ | |_ \-//
_|_ ___) |__| \_/ _|_ | // \
//-----\\
//---------\\
isugifNF/polishCLR v1.0.0
----------------------------------------------------
Usage:
The typical command for running the pipeline are as follows:
nextflow run main.nf --primary_assembly "*fasta" --illumina_reads "*{1,2}.fastq.bz2" --pacbio_reads "*_subreads.bam" -resume
Mandatory arguments:
--illumina_reads Paired end Illumina reads, to be used for Merqury QV scores, and FreeBayes polish primary assembly
--pacbio_reads PacBio reads in bam format, to be used to Arrow polish primary assembly
--mitochondrial_assembly Mitochondrial assembly will be concatenated to the assemblies before polishing [default: false]
Either FALCON (or FALCON-Unzip) assembly:
--primary_assembly Genome assembly fasta file to polish
--alternate_assembly If alternate/haplotig assembly file is provided, will be concatenated to the primary assembly before polishing [default: false]
--falcon_unzip If primary assembly has already undergone FALCON-Unzip [default: false]. If true, will Arrow polish once instead of twice.
Pick Step 1 (arrow, purgedups) or Step 2 (Arrow, FreeBayes, FreeBayes)
--step Run step 1 or step 2 (default: 1)
Optional modifiers
--species If a string is given, rename the final assembly by species name [default:false]
--k kmer to use in MerquryQV scoring [default:21]
--same_specimen If Illumina and PacBio reads are from the same specimen [default: true].
--meryldb Path to a prebuilt Meryl database, built from the Illumina reads. If not provided, then build.
Optional configuration arguments
--parallel_app Link to parallel executable [default: 'parallel']
--bzcat_app Link to bzcat executable [default: 'bzcat']
--pigz_app Link to pigz executable [default: 'pigz']
--meryl_app Link to meryl executable [default: 'meryl']
--merqury_sh Link to merqury script [default: '$MERQURY/merqury.sh']
--pbmm2_app Link to pbmm2 executable [default: 'pbmm2']
--samtools_app Link to samtools executable [default: 'samtools']
--gcpp_app Link to gcpp executable [default: 'gcpp']
--bwamem2_app Link to bwamem2 executable [default: 'bwa-mem2']
--freebayes_app Link to freebayes executable [default: 'freebayes']
--bcftools_app Link to bcftools executable [default: 'bcftools']
--merfin_app Link to merfin executable [default: 'merfin']
Optional parameter arguments
--parallel_params Parameters passed to parallel executable [default: ' -j 2 ']
--pbmm2_params Parameters passed to pbmm2 align [default: '']
--minimap2_params Parameters passed to minimap2 -xmap-pb or -xasm5 [default: '']
--gcpp_params Parameters passed to gcpp [default: ' -x 10 -X 120 -q 0 ']
--bwamem2_params Parameters passed to bwamem2 [default: ' -SP ']
--freebayes_params Parameters passed to freebayes [default: ' --min-mapping-quality 0 --min-coverage 3 --min-supporting-allele-qsum 0 --ploidy 2 --min-alternate-fraction 0.2 --max-complex-gap 0 ']
--purge_dups_params Parameters passed to purge_dups [default: ' -2 -T p_cufoffs ']
--busco_params Parameters passed to busco [default: ' -l insecta_odb10 -m genome -f ']
Optional arguments:
--outdir Output directory to place final output [default: 'PolishCLR_Results']
--clusterOptions Cluster options for slurm or sge profiles [default slurm: '-N 1 -n 40 -t 04:00:00'; default sge: ' ']
--threads Number of CPUs to use during each job [default: 40]
--queueSize Maximum number of jobs to be queued [default: 50]
--account Some HPCs require you supply an account name for tracking usage. You can supply that here.
--help This usage statement.
--check_software Check if software dependencies are available.
Example
For step-by-step instructions and easily accessible test datasets, please View the READ THE DOCs (RTD) Manual for PolishCLR.
Example input data for each of the three input cases from Helicoverpa zea on Ag Data Commons: https://data.nal.usda.gov/dataset/data-polishclr-example-input-genome-assemblies. SRAs from NCBI for pacbio and illumina data are available through the BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA804956
# If you have installed dependencies in a miniconda environment
source activate ${PWD}/env/polishCLR_env
SP_DIR=/project/ag100pest/Helicoverpa_zea_male
## === Step 1 (up to purge_dups)
nextflow run isugifNF/polishCLR -r main \
--primary_assembly "${SP_DIR}/Falcon/4-polish/cns-output/cns_p_ctg.fasta" \
--alternate_assembly "${SP_DIR}/Falcon/4-polish/cns-output/cns_h_ctg.fasta" \
--mitochondrial_assembly "${SP_DIR}/MT_Contig/Hzea_mtDNA_contig.fasta" \
--illumina_reads "${SP_DIR}/PolishingData/JDRP*{R1,R2}.fastq.bz2" \
--pacbio_reads "${SP_DIR}/RawData/m*.subreads.bam" \
--species "Hzea" \
--k "21" \
--falcon_unzip true \
--step 1 \
--busco_lineage "lepideoptera_odb10" \
-resume \
-profile ceres
### I often submit these as two separate slurm scripts
## === Step 2
nextflow run isugifNF/polishCLR -r main \
--primary_assembly "PolishCLR_Results/Step_1/02_Purge_Dups/primary_purged.fa" \
--alternate_assembly "PolishCLR_Results/Step_1/02_Purge_Dups/haps_purged.fa" \
--mitochondrial_assembly "${SP_DIR}/MT_Contig/Hzea_mtDNA_contig.fasta" \
--illumina_reads "${SP_DIR}/PolishingData/JDRP*{R1,R2}.fastq.bz2" \
--pacbio_reads "${SP_DIR}/RawData/m*.subreads.bam" \
--species "Hzea" \
--k "21" \
--falcon_unzip true \
--step 2 \
-resume \
-profile ceres
Key Outputs are found in
- PolishCLR_Results/Step_1/02_BUSCO/primary_purged/ ## BUSCO stats after purge_dups
- PolishCLR_Results/Step_1/02_Purge_Dups/primary_purged.fa ## Primary assembly after Step 1
- PolishCLR_Results/Step_1/02_Purge_Dups/haps_purged.fa ## Alternate assembly after Step 1
- PolishCLR_Results/Step_2/*_bbstat/ ## Length and number distributions through each process of Step 2
- PolishCLR_Results/Step_2/*_QV/ ## QV and Completeness stats with merfin and merqury for each process of Step 2
- PolishCLR_Results/Step_2/06_FreeBayesPolish/p_Step_2_06_FreeBayesPolish_consensus.fasta ## Final primary fasta (no mito)
- PolishCLR_Results/Step_2/06_FreeBayesPolish/a_Step_2_06_FreeBayesPolish_consensus.fasta ## Final alternate fasta (no mito)
Step 1
[ea/f78cb8] process > RENAME_PRIMARY (1) [100%] 1 of 1, cached: 1 ✔
[53/770510] process > MERGE_FILE_00 (1) [100%] 1 of 1, cached: 1 ✔
[34/a4b7ac] process > bz_to_gz (1) [100%] 1 of 1, cached: 1 ✔
[3e/0af766] process > meryl_count (1) [100%] 2 of 2, cached: 2 ✔
[76/a26404] process > meryl_union [100%] 1 of 1, cached: 1 ✔
[7c/d4916c] process > meryl_peak [100%] 1 of 1, cached: 1 ✔
[ef/c58401] process > MerquryQV_00 (1) [100%] 1 of 1, cached: 1 ✔
[cd/3ad9c7] process > bbstat_00 (1) [100%] 1 of 1, cached: 1 ✔
[3e/dd32f5] process > bam_to_fasta (1) [100%] 1 of 1, cached: 1 ✔
[00/1b1177] process > SPLIT_FILE_02 (1) [100%] 1 of 1, cached: 1 ✔
[78/df2d30] process > PURGE_DUPS_02 (1) [100%] 1 of 1, cached: 1 ✔
[5f/dec926] process > BUSCO (2) [100%] 2 of 2 ✔
Completed at: 21-Dec-2021 10:45:52
Duration : 51m 32s
CPU hours : 3.9 (63.3% cached)
Succeeded : 2
Cached : 12
Step 2
executor > local (1), slurm (2681)
[d9/b48b2c] process > RENAME_PRIMARY (1) [100%] 1 of 1 ✔
[25/b9acec] process > MERGE_FILE_00 (1) [100%] 1 of 1 ✔
[94/ff9db2] process > bz_to_gz (1) [100%] 1 of 1 ✔
[2c/bd2fc0] process > meryl_count (1) [100%] 2 of 2 ✔
[00/b4d5aa] process > meryl_union [100%] 1 of 1 ✔
[62/116067] process > meryl_peak [100%] 1 of 1 ✔
[76/7ecb59] process > MerquryQV_00 (1) [100%] 1 of 1 ✔
[12/ee4395] process > bbstat_00 (1) [100%] 1 of 1 ✔
[93/7d56c3] process > ARROW_04:create_windows (1) [100%] 1 of 1 ✔
[3a/15bd43] process > ARROW_04:pbmm2_index (1) [100%] 1 of 1 ✔
[05/75aae9] process > ARROW_04:pbmm2_align (1) [100%] 1 of 1 ✔
[6b/92ea05] process > ARROW_04:gcpp_arrow (3) [100%] 882 of 882 ✔
[55/29df60] process > ARROW_04:meryl_genome (1) [100%] 1 of 1 ✔
[0f/8eb0eb] process > ARROW_04:combineVCF (1) [100%] 1 of 1 ✔
[9b/a8433d] process > ARROW_04:reshape_arrow (1) [100%] 1 of 1 ✔
[2f/bb106e] process > ARROW_04:merfin_polish (1) [100%] 1 of 1 ✔
[e5/609325] process > ARROW_04:vcf_to_fasta (1) [100%] 1 of 1 ✔
[d6/0b30fa] process > MerquryQV_04 (1) [100%] 1 of 1 ✔
[4c/dd5ce5] process > bbstat_04 (1) [100%] 1 of 1 ✔
[5c/7d00a5] process > FREEBAYES_05:create_windows... [100%] 1 of 1 ✔
[62/269cb4] process > FREEBAYES_05:meryl_genome (1) [100%] 1 of 1 ✔
[43/329d5d] process > FREEBAYES_05:align_shortrea... [100%] 1 of 1 ✔
[15/ece2b2] process > FREEBAYES_05:freebayes (754) [100%] 882 of 882 ✔
[ab/47faff] process > FREEBAYES_05:combineVCF (1) [100%] 1 of 1 ✔
[8b/5461c2] process > FREEBAYES_05:merfin_polish (1) [100%] 1 of 1 ✔
[ea/0a6fb3] process > FREEBAYES_05:vcf_to_fasta (1) [100%] 1 of 1 ✔
[4a/c67e0a] process > MerquryQV_05 (1) [100%] 1 of 1 ✔
[57/f661d4] process > bbstat_05 (1) [100%] 1 of 1 ✔
[a5/5e8166] process > FREEBAYES_06:create_windows... [100%] 1 of 1 ✔
[ea/ccf140] process > FREEBAYES_06:meryl_genome (1) [100%] 1 of 1 ✔
[40/d1cbd4] process > FREEBAYES_06:align_shortrea... [100%] 1 of 1 ✔
[f3/a7920f] process > FREEBAYES_06:freebayes (514) [100%] 882 of 882 ✔
[ff/c3c29b] process > FREEBAYES_06:combineVCF (1) [100%] 1 of 1 ✔
[9f/462b6c] process > FREEBAYES_06:merfin_polish (1) [100%] 1 of 1 ✔
[a0/3218e0] process > FREEBAYES_06:vcf_to_fasta (1) [100%] 1 of 1 ✔
[f8/0f5b7c] process > MerquryQV_06 (1) [100%] 1 of 1 ✔
[e8/09d9db] process > bbstat_06 (1) [100%] 1 of 1 ✔
[12/04a0db] process > SPLIT_FILE_07 (1) [100%] 1 of 1 ✔
Completed at: 23-Dec-2021 11:45:16
Duration : 21h 33m 40s
CPU hours : 195.0
Succeeded : 2'682
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., Lee, C., Ko, B. J., Chaisson, M., Gedman, G. L., Cantin, L. J., Thibaud-Nissen, F., Haggerty, L., Bista, I., Smith, M., . . . Jarvis, E. D. (2021). Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856), 737-746. https://doi.org/10.1038/s41586-021-03451-0
Rhie, A., Walenz, B. P., Koren, S., & Phillippy, A. M. (2020). Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol, 21(1), 245. https://doi.org/10.1186/s13059-020-02134-9.
Formenti, G., Rhie, A., Balacco, J., Haase, B., Mountcastle, J., Fedrigo, O., Brown, S., Capodiferro, M. R., Al-Ajli, F. O., Ambrosini, R., Houde, P., Koren, S., Oliver, K., Smith, M., Skelton, J., Betteridge, E., Dolucan, J., Corton, C., Bista, I., . . . Vertebrate Genomes Project, C. (2021). Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Genome Biol, 22(1), 120. https://doi.org/10.1186/s13059-021-02336-9
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