In Geneious 2023.2 or later, the de novo assembly advisor can recommend the most appropriate assembly algorithm for your data. Click "Let us Help!" in the de novo assembly window to start an interactive questionnaire that will guide you though the following decision tree.
Support for each decision in the tree can be found in the validation table below.
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What type of reads do you want to assemble? Sanger |
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Assembler |
References |
Summary |
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Geneious |
Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology |
Assembly of ITS amplicon via Geneious assembler |
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Assembly of full-length mastrevirus genome with Sanger sequences using Geneious assembler |
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Assembly of full-length mastrevirus genome with Sanger sequences using Geneious assembler |
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Does your genome consists of complex elements such as repeats and/or are you working with ESTs? Yes |
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Assembler |
References |
Summary |
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Mira |
miraEST assembler for mRNA transcript sequences reconstruction |
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Benchmarking of EST assemblers whereby MIRA was shown to have high sensitivity and specificity in transcriptome assembly |
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Comparing de novo assemblers for 454 transcriptome data - BMC Genomics |
Benchmarking of transcriptome assemblers showing that Mira works best with normalized transcriptome sequence data |
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Are you working with metagenomic and/or RNA dataset? Yes |
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Assembler |
References |
Summary |
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Geneious |
Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology |
Assembly of ITS amplicon via Geneious assembler |
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Processing and assembling of raw 18S V9 and 12S rRNA reads using Geneious assembler |
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Do you expect your coverage to be low or biased? Yes |
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Assembler |
References |
Summary |
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Geneious |
The (non) accuracy of mitochondrial genomes for family‐level phylogenetics in Erebidae (Lepidoptera) |
Assembly of low coverage Erebidae mitochondrial genomes |
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Is speed more important to you than sensitivity? Yes |
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Assembler |
References |
Summary |
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Velvet |
Using the Velvet de novo assembler for short-read sequencing technologies |
Rapid short-read de novo assembler capable of producing comparable long continuous contigs and gapped assemblies of contigs |
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Benchmarking of de novo assembler algorithms showing that Velvet has a low CPU time consumption when assembling 2D reads of E. coli datasets with an average N50 value of 10,000 bp |
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Study of de novo assembler demonstrated that Velvet provides high scalability for large data, performs well on single-end eukaryotic data sets and has low assembling time |
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What is the size of your sequenced genome? >100 Mbp |
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Assembler |
References |
Summary |
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Velvet |
*Using the Velvet de novo assembler for short-read sequencing technologies |
Rapid short-read de novo assembler capable of producing comparable long continuous contigs and gapped assemblies of contigs |
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Denovo assembly of strawberry genome using Velvet |
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Study of de novo assembler demonstrated that Velvet provides high scalability for large data, performs well on single-end eukaryotic data sets and has low assembling time |
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Caenorhabditis elegans genome (100 Mb) de novo assembly with Velvet achieving ~95% coverage with as low as 35X read depth |
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What type of reads do you want to assemble? Long read |
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Assembler |
References |
Summary |
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Flye |
Benchmark of SMS (Single-molecule-sequencing) assemblers showed that Flye is capable of assembling long error-prone reads using repeat graphs |
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Construction of a chromosome-scale long-read reference genome assembly for potato |
Assembling nanopore reads from whole-genome shotgun sequencing of cultivated potato with Flye |
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Efficient assembly of nanopore reads via highly accurate and intact error correction |
Comparison of nanopore assemblers demonstrated that Flye produces high quality contigs with high NG50 and NGA50 and small numbers of misassemblies |
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F1000Research Article: Benchmarking of long-read assemblers for prokaryote whole genome sequencing. |
Benchmarking long-reads assemblers for prokaryote whole genome sequencing showing that Flye is reliable, robut and made the smallest sequence error |
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What type of reads do you want to assemble? Hybrid |
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Assembler |
References |
Summary |
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SPAdes |
https://academic.oup.com/bioinformatics/article/32/7/1009/1743807 |
HYBRIDSPADES algorithm for assembling short and long reads |
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Assembly of PacBio and Illumina reads from Photorhabdus khanii genone sequencing |
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Genome scaffolding using long reads to bridge and merge contigs from short-read assembly |
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