LONG-READ-TOOLS is a catalogue of software packages designed for the analysis of long read sequencing data. This website provides extensive materials for processing of long reads, where you are able to filter based on categories and sequencing technology.
The Wellcome Sanger Institute is a world leader in genome research that delivers insights into human, evolutionary and pathogen biology. This website provides helpful tools for genomic data processing, short descriptions of their uses, as well as available manuals.
This website developed by Dr. Martti T. Tammi and a team of qualified professionals provides tutorials and other useful information related to genomics/bioinformatics. Specifically linked here is a page that is a database of bioinformatics software tools and resources. Additionally, check out this page that focuses on free whole genome assembly (WGA) analysis tools.
In this tutorial you will perform a de novo assembly of short-read next-generation sequencing data. You’ll learn about how to work with paired-end data and how to check the quality of your assembly against a reference sequence. This is a simple click-button approach, but can be useful for new learners to genomic data processing.
The SEQanswers website was created in order to provide next-generation sequencing tools and information. This link lists tools and information for variant analysis and genome assembly.
CD Genomics aims to provide the research community with high-quality next-generation sequencing, PacBio SMRT sequencing, Oxford Nanopore sequencing, and microarray services. This page is a guide to De Novo genome assembly.
Melbourne Bioinformatics developed a protocol that discusses and outlines the process of de novo assembly for small to medium sized genomes.
Genome Assembly Tools (GitHub)
This helpful GitHub page, created by postdoc Nadège Guiglielmoni at Universität zu Köln, lists genome assembly tools based on those presented in the review: "A deep dive into genome assemblies of non-vertebrate animals." Guiglielmoni N, Rivera-Vicéns R, Koszul R, Flot J-F. Peer Community Journal, 2022.
The website linked above gives presentation slides, as well as an overview of de novo assembly processes for genomic data.
BioStars is a discussion forum, which focuses on bioinformatics, computational genomics and biological data analysis. Researchers can look for questions/posts related to the topic they are interested in, or create new discussions to gain feedback from experts and learners in their respective fields.
The SourceForge platform provides information for most software currently available in bioinformatics and other fields of study. Searching can be done based on programming language, operating system, and translations, among others.
Chen, B., Zhou, Z., Ke, Q. et al. The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies. Sci Data 6, 188 (2019). https://doi.org/10.1038/s41597-019-0194-3
Dida, F., & Yi, G. (2021). Empirical evaluation of methods for de novo genome assembly. PeerJ. Computer science, 7, e636. https://doi.org/10.7717/peerj-cs.636
Konrad Paszkiewicz, David J. Studholme, De novo assembly of short sequence reads, Briefings in Bioinformatics, Volume 11, Issue 5, September 2010, Pages 457–472, https://doi.org/10.1093/bib/bbq020
Lischer, H. E. L., & Shimizu, K. K. (2017). Reference-guided de novo assembly approach improves genome reconstruction for related species. BMC bioinformatics, 18(1), 474. https://doi.org/10.1186/s12859-017-1911-6
Miller, J.R., Zhou, P., Mudge, J. et al. Hybrid assembly with long and short reads improves discovery of gene family expansions. BMC Genomics 18, 541 (2017). https://doi.org/10.1186/s12864-017-3927-8
Morisse, P., Marchet, C., Limasset, A. et al. Scalable long read self-correction and assembly polishing with multiple sequence alignment. Sci Rep 11, 761 (2021). https://doi.org/10.1038/s41598-020-80757-5
Morisse, P., Lecroq, T., & Lefebvre, A. (2020). Long-read error correction: a survey and qualitative comparison. bioRxiv.
YongKiat Wee, Salma Begum Bhyan, Yining Liu, Jiachun Lu, Xiaoyan Li, Min Zhao, The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing, Briefings in Functional Genomics, Volume 18, Issue 1, January 2019, Pages 1–12, https://doi.org/10.1093/bfgp/ely037
de novo assembly by Rayan Chikhi
This presentation created for a de novo assembly workshop by Rayan Chikhi while completing a Postdoc at Penn State, provides detailed background information and informative diagrams/figures on de novo assembly processes.
Finding the appropriate method, with a special focus on: Mapping and alignment by Philip Clausen
This presentation, titled "Finding the appropriate method, with a special focus on: Mapping and alignment" by Philip Clausen, is useful for gaining more insight on alignment and mapping processes of genomic data.
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