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What is Semblans?

Semblans a tool that enables the automatic assembly of de novo transcriptomes for non-model organisms.

Through the collation of several external packages and the leveraging of C++ data streaming performance, Semblans streamlines the necessary pre-processing, quality control, assembly, and post-assembly steps, allowing a ‘hands-off’ assembly process without loss to versatility.

Semblans workflow

Shown here is a graphical representation of the Semblans pipeline's workflow.

External packages / databases

Semblans employs a variety of powerful third-party tools in its pipeline. The user is encouraged to learn about these packages individually on their own time. These are listed below:

• Rcorrector
  • Song, L., Florea, L. Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads. GigaSci 4, 48 (2015). https://doi.org/10.1186/s13742-015-0089-y
• Trimmomatic
  • Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170. https://doi.org/10.1093/bioinformatics/btu170
• Kraken2
  • Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019). https://doi.org/10.1186/s13059-019-1891-0
• Trinity
  • Haas, B., Papanicolaou, A., Yassour, M. et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8, 1494–1512 (2013). https://doi.org/10.1038/nprot.2013.084
• Salmon
  • Patro, R., Duggal, G., Love, M. et al. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14, 417–419 (2017). https://doi.org/10.1038/nmeth.4197
• STAR
  • Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PMID: 23104886; PMCID: PMC3530905.
• Corset
  • Davidson, N.M., Oshlack, A. Corset: enabling differential gene expression analysis for de novoassembled transcriptomes. Genome Biol 15, 410 (2014). https://doi.org/10.1186/s13059-014-0410-6
• TransDecoder
  • Haas, BJ. https://github.com/TransDecoder/TransDecoder, software version v5.7.0
• SRA-Tools
  • https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software and the SRA Toolkit Development Team
• BLAST+
  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009 Dec 15;10:421. doi: 10.1186/1471-2105-10-421. PMID: 20003500; PMCID: PMC2803857.
• Diamond
  • Buchfink B, Reuter K, Drost HG, "Sensitive protein alignments at tree-of-life scale using DIAMOND", Nature Methods 18, 366–368 (2021). doi:10.1038/s41592-021-01101-x
• FastQC
  • Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
• HMMER
  • Howard Hughes Medical Institute (2020), http://hmmer.org/, Software version: HMMER 3.3.2 (Nov 2020)
• Panther DB, Scoring Tool
  • Paul D. Thomas, Dustin Ebert, Anushya Muruganujan, Tremayne Mushayahama, Laurent-Philippe Albou and Huaiyu Mi Protein Society. 2022;31(1):8-22. doi:10.1002/pro.4218

External libraries

In addition to external packages, Semblans employs external C++ libraries for many of its under-the-hood operations. These are listed below:

• Boost Libraries Software version: Boost 1.81.0
  • Filesystem
  • System
  • Regex
  • DLL
• rapidXML Software version: RapidXML 1.13.0
• libconfini Software version: libconfini 1.16.4
• libcurl Software version: Curl 8.1.2