AssemblyQC is a Nextflow pipeline which evaluates assembly quality with well established tools and presents the results in a unified html report.

Reference:

Rashid, U., Wu, C., Shiller, J., Smith, K., Crowhurst, R., Davy, M., Chen, T.-H., Carvajal, I., Bailey, S., Thomson, S., & Deng, C.H. (2024). AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality. Bioinformatics. DOI 10.1093/bioinformatics/btae477. GitHub https://github.com/Plant-Food-Research-Open/assemblyqc.

FCS-adaptor detects adaptor and vector contamination in genome sequences.

Reference:

https://github.com/ncbi/fcs

Version: 0.5.0

FCS-GX detects contamination from foreign organisms in genome sequences.

Reference:

Alexander Astashyn, Eric S Tvedte, Deacon Sweeney, Victor Sapojnikov, Nathan Bouk, Victor Joukov, Eyal Mozes, Pooja K Strope, Pape M Sylla, Lukas Wagner, Shelby L Bidwell, Karen Clark, Emily W Davis, Brian Smith-White, Wratko Hlavina, Kim D Pruitt, Valerie A Schneider, Terence D Murphy bioRxiv 2023.06.02.543519; doi: 10.1101/2023.06.02.543519, GitHub: https://github.com/ncbi/fcs

Version: 0.5.4

DB Version: 2023-01-24

Note:

This report dynamically loads '*.fcs.gx.krona.html' files from the 'ncbi_fcs_gx' folder under the output directory. These files should also be moved when moving the report's HTML file.

A script to calculate a basic set of metrics from a genome assembly.

Reference:

https://github.com/KorfLab/Assemblathon

Version: github/PlantandFoodResearch/assemblathon2-analysis/a93cba2

Warning:

Contig-related stats are based on the assumption that the assemblathon_stats_n_limit (100) parameter is specified correctly. If you are not certain of the value of the n_limit parameter, please ignore the contig-related stats.

A fast and exhaustive tool for summary statistics.

Reference:

Giulio Formenti, Linelle Abueg, Angelo Brajuka, Nadolina Brajuka, Cristóbal Gallardo-Alba, Alice Giani, Olivier Fedrigo, Erich D Jarvis, Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs, Bioinformatics, Volume 38, Issue 17, September 2022, Pages 4214–4216, 10.1093/bioinformatics/btac460

Version: 1.3.6

A tool to calculate a basic set of statistics about features contained in GFF3 files.

Reference:

Gremme G, Steinbiss S, Kurtz S. GenomeTools: a comprehensive software library for efficient processing of structured genome annotations. IEEE/ACM Trans Comput Biol Bioinform. 2013 May-Jun;10(3):645-56. doi: 10.1109/TCBB.2013.68. PMID: 24091398.

Version: 1.6.5

BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs.

Reference:

Manni M., Berkeley M.R., Seppey M., Simao F.A., Zdobnov E.M. 2021. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. arXiv:2106.11799 [q-bio] [Internet]. Available from: arxiv.org/abs/2106.11799

Version: 5.7.1

BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. GFFREAD is used to obtain protein sequences from assembly FASTA and annotation GFF3 files.

Reference:

Manni M., Berkeley M.R., Seppey M., Simao F.A., Zdobnov E.M. 2021. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. arXiv:2106.11799 [q-bio] [Internet]. Available from: arxiv.org/abs/2106.11799

Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: 10.12688/f1000research.23297.2. PMID: 32489650; PMCID: PMC7222033.

Version: 5.7.1 (BUSCO), 0.12.7 (GFFREAD)

A toolkit to identify and visualise telomeric repeats for the Darwin Tree of Life genomes.

Reference:

https://github.com/tolkit/telomeric-identifier

Version: 0.2.41

LTR Assembly Index (LAI) is a reference-free genome metric that evaluates assembly continuity using LTR-RTs. LTR retrotransposons (LTR-RTs) are the predominant interspersed repeat that is poorly assembled in draft genomes. Correcting for LTR-RT amplification dynamics, LAI is independent of genome size, genomic LTR-RT content, and gene space evaluation metrics such as BUSCO. LAI = Raw LAI + 2.8138 × (94 – whole genome LTR identity). The LAI is set to 0 when raw LAI = 0 or the adjustment produces a negative value. Raw LAI = (Intact LTR element length / Total LTR sequence length) * 100

Reference:

Shujun Ou, Jinfeng Chen, Ning Jiang, Assessing genome assembly quality using the LTR Assembly Index (LAI), Nucleic Acids Research, Volume 46, Issue 21, 30 November 2018, Page e126, 10.1093/nar/gky730

Version: beta3.2

Kraken2 assigns taxonomic labels to sequencing reads for metagenomics projects.

Reference:

Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019). 10.1186/s13059-019-1891-0

Version: 2.1.2

Note:

This report dynamically loads '*.kraken2.krona.html' files from the 'kraken2' folder under the output directory. These files should also be moved when moving the report's HTML file.

Hi-C contact mapping experiments measure the frequency of physical contact between loci in the genome. The resulting dataset, called a “contact map,” is represented using a two-dimensional heatmap where the intensity of each pixel indicates the frequency of contact between a pair of loci.

References:

fastp Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, September 2018, Pages i884–i890, 10.1093/bioinformatics/bty560

BWA Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv: 1303.3997.

SAMBLASTER Gregory G. Faust, Ira M. Hall, SAMBLASTER: fast duplicate marking and structural variant read extraction, Bioinformatics, Volume 30, Issue 17, September 2014, Pages 2503–2505, 10.1093/bioinformatics/btu314

SAMtools Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li, Twelve years of SAMtools and BCFtools, GigaScience, Volume 10, Issue 2, February 2021, giab008, 10.1093/gigascience/giab008

Juicebox.js Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL. Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. Cell Syst. 2018 Feb 28;6(2):256-258.e1. 10.1016/j.cels.2018.01.001. Epub 2018 Feb 7. PMID: 29428417; PMCID: PMC6047755.

Version: 2.4.3

Notes:

• The Hi-C contact map is only loaded when the report is opened through a HTTP(s) server and all the necessary permissions are in place. The contact map '.hic' file is stored in the 'hic' folder under the output directory. It can be visualized with Juicebox.
• This report dynamically loads content from the 'hic' folder under the output directory including '*.hic', '*.html', 'bedpe/' and 'hicqc/'. These files and folders should also be moved when moving the report's HTML file.

Circos facilitates the identification and analysis of similarities and differences arising from comparisons of genomes. The genome-wide alignments are performed with MUMMER.

References:

Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., ... & Marra, M. A. (2009). Circos: an information aesthetic for comparative genomics. Genome research, 19(9), 1639-1645. 10.1101/gr.092759.109

Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome alignment system. PLoS Comput Biol. 2018 Jan 26;14(1):e1005944. 10.1371/journal.pcbi.1005944

Versions: v0.69-8 (CIRCOS), 4.0.0rc1 (MUMMER)

Notes:

• Alignments within a distance of 1000000bp have been bundled together.
• After bundling, any bundle smaller than 1000000bp has been filtered out.
• The sequence labels shown on the plot are based on the labelling file provided to the pipeline. These labels may or may not be same as the sequence IDs in the corresponding FASTA files.

The genome-wide alignments are performed with MUMMER.

References:

Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., ... & Marra, M. A. (2009). Circos: an information aesthetic for comparative genomics. Genome research, 19(9), 1639-1645. https://doi.org/10.1101/gr.092759.109

Version: 4.0.0rc1 (MUMMER)

Notes:

• Alignments within a distance of 1000000bp have been bundled together.
• After bundling, any bundle smaller than 1000000bp has been filtered out.
• The sequence labels shown on the plot are based on the labelling file provided to the pipeline. These labels may or may not be same as the sequence IDs in the corresponding FASTA files.

Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies. The genome-wide alignments are performed with Minimap2.

References:

Goel M, Schneeberger K. 2022. plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics. 2022 May 13;38(10):2922-2926. doi: 10.1093/bioinformatics/btac196. PMID: 35561173; PMCID: PMC9113368.

Goel M, Sun H, Jiao WB, Schneeberger K. 2019. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019 Dec 16;20(1):277. doi: 10.1186/s13059-019-1911-0. PMID: 31842948; PMCID: PMC6913012.

Li H. 2021. New strategies to improve minimap2 alignment accuracy, Bioinformatics, Volume 37, Issue 23, December 2021, Pages 4572–4574, doi: 10.1093/bioinformatics/btab705

Versions: 1.1.1 (PLOTSR), 1.7.0 (SYRI), 2.28-r1209 (MINIMAP2)

Note:

This report dynamically loads '*.on.*.all/' folders from the 'synteny' folder under the output directory. These folders should also be moved when moving the report's HTML file.

Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this purpose.

References:

Rhie, A., Walenz, B.P., Koren, S. et al. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol 21, 245 (2020). doi: 10.1186/s13059-020-02134-9

Version: 1.3