In Geneious 2024 or later, the Map-to-Reference assembly advisor can recommend the most appropriate mapping algorithm for your data. Click "Let us Help!" in the Map-to-Reference 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.
|
What type of reads are you trying to map? Sanger
|
||
| Mapper | Geneious | Summary |
| References | https://www.nature.com/articles/s41598-021-01589-5 |
Geneious mapper was used to map raw foraminiferal COI Sanger sequences
|
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6221210/ |
Geneious mapper was used to map Plasmodium vivax 18S rRNA Sanger sequences
|
|
| https://www.frontiersin.org/articles/10.3389/fmicb.2021.770787/full |
Geneious RNA mapper was used to map Sanger sequences to mycovirus genome
|
|
| https://www.sciencedirect.com/science/article/pii/S2666979X2200057X |
Long range PCR of LINE (Long interspersed nuclear elements) sequences were aligned using Geneious mapper
|
|
|
Does your reference sequence consist of complex elements such as tandem repeats? Yes
|
||
| Mapper | BBMap | Summary |
| References | https://www.nature.com/articles/s41586-022-05256-1 |
BBMap was used to align Illumina reads to Bord's genome where tandem direct repeat sequences are prevalent
|
| https://www.frontiersin.org/articles/10.3389/fmicb.2017.01448/full |
BBMap was used to alignment of PacBio and Illumina reads to Burkholderia pseudomallei genome, a bacterium which contains two large circular chromosomes, very high G+C content of 68–69%, highly repetitive regions and substantial genomic diversity
|
|
|
Does your reference sequence consist of complex elements such as tandem repeats? Yes
|
||
| Mapper | minimap2 | Summary |
| References | https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02831-7 |
Benchmarking paper showed that minimap2 have the highest accuracy when aligning a repetitive dataset with high diversity generated with Illumina sequencing technology
|
|
Does your reference sequence consist of complex elements such as tandem repeats? No
|
||
| Mapper | Geneious | Summary |
| References | https://academic.oup.com/gbe/article/5/9/1661/557212 |
Mapping of Illumina HiSeq reads to Polytomella magna mitochondrial DNA made up entirely palindromes via Geneious mapper resulting in complete linear-mapping mitochondrial genome with telomeres
|
| https://www.nature.com/articles/s41598-022-05706-w |
Mapping of Illumina reads using Geneious mapper helped identify insertion of viral and human origin in the Hepatitis E virus genome
|
|
| https://www.nature.com/articles/s41598-022-10720-z |
Mapping of Illumina MiSeq with Geneious mapper eads resulting in the first whole genome sequences of Vibrio harveyi isolated from European sea bass
|
|
|
Does your reference sequence consist of complex elements such as tandem repeats? No
|
||
| Mapper | Bowtie2 | Summary |
| References | https://www.cell.com/cell/pdf/S0092-8674(21)00585-7.pdf |
Bowtie2 was utilised to map Illumina reads to human genome hg38 and microbial genome in a metagenomic study
|
| https://www.frontiersin.org/articles/10.3389/fevo.2020.00105/full#S10 |
This paper showed that Bowtie2 aligner substantially reduce computational times and increase sensitivity when mapping HiSeq ancient DNA reads
|
|
|
Are you interested in identifying structural variants? Yes/No
|
||
| Mapper | minimap2 | Summary |
| References | https://www.nature.com/articles/s41467-023-35996-1 |
PacBio CLR, HiFi, and Nanopore reads were aligned to human GRCh37 genome via minimap2 to help detect structural variants
|
| https://www.nature.com/articles/s41467-018-07271-1 |
minimap2 was used to map Nanopore reads to access structural integrity of large and repeat-rich plant genomes
|
|
| https://www.biorxiv.org/content/10.1101/2022.04.04.487055v1.full.pdf |
minimap2 was used to map PacBio and Oxford Nanopore reads to the human genome to help identify mosaic structural variants
|
|
| https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000682 |
Nanopore reads were mapped to Escherichia coli genome with the minimap2 whereby routine rearrangements occur in the genome resulting in structural variants
|
|
| https://academic.oup.com/bioinformatics/article/37/23/4572/6384570 |
Original paper - Minimap v2.22 accurately maps long reads to highly repetitive regions and align through indels up to 100 kb
|
|
|
Are you interested in identifying structural variants? Yes/No
|
||
| Mapper | Geneious | Summary |
| References | https://academic.oup.com/ve/article/6/1/vez060/5716172 |
PacBio reads were mapped to AcMNPV virus genome via Geneious mapper to detect structural variants
|
| https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000682 |
PacBio and Illumina reads were mapped to Escherichia coli genome with the Geneious mapper whereby routine rearrangements occur in the genome resulting in structural variants
|
|
|
Are you interested in identifying structural variants? Yes/No
|
||
| Mapper | Geneious RNA | Summary |
| References | https://www.cell.com/iscience/pdf/S2589-0042(23)00857-X.pdf |
Geneious RNA mapper was used to map HiSeq reads to the MERS-CoV genome to study the complex genome organization and expression network of MERS-CoV
|
|
Are you interested in identifying structural variants? No
|
||
| Mapper | BBMap | Summary |
| References | https://academic.oup.com/ve/article/6/1/vez060/5716172 |
BBMap was used to map metagenome-assembled HiFi reads to provide insights into metabolic potential of uncultivated members of Armatimonadota
|
| https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000682 |
BBMap was used to alignment of PacBio and Illumina reads to Burkholderia pseudomallei genome, a bacterium with highly repetitive regions and substantial genomic diversity
|
|
|
Are you interested in annotating splice junctions? Yes/No
|
||
| Mapper | STAR | Summary |
| References | https://www.nature.com/articles/nmeth.2722 |
This study showed that STAR achieved high accuracy of splice-detection when mapping real human and mouse transcriptome data, and simulated RNA-seq data
|
| https://www.nature.com/articles/nmeth.4106 |
Benchmarking of RNA-seq aligners showed that STAR aligner is consistently accurate in identifying intron boundaries in human and Plasmodium falciparum genomes
|
|
| https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.13312 |
Novel splice junctions were discovered with STAR when mapping RNA-seq reads the Arabidopsis thaliana genome
|
|
| https://www.sciencedirect.com/science/article/pii/S0888754319307517 |
STAR was used to map RNA-seq reads to hg19 and hg38, to identify splice junctions
|
|
|
Are you interested in annotating splice junctions? No
|
||
| Mapper | Geneious RNA | Summary |
| References | https://www.nature.com/articles/s41598-018-35654-3 |
Illumina generated RNA-seq libraries were mapped to chloroplast genomes from a variety of organisms via Geneious RNA to show that RNA-seq data can be used to assemble chloroplast genomes
|
| https://www.cell.com/iscience/pdf/S2589-0042(23)00857-X.pdf |
Geneious RNA mapper was used to map HiSeq reads to the MERS-CoV genome to study the complex genome organization and expression network of MERS-CoV
|
|
| https://journals.asm.org/doi/full/10.1128/mbio.01610-20 |
Geneious RNA mapper was used to map MiSeq reads to the SARS-CoV-2 genome to detect a variety of genomic changes
|
|
| https://journals.asm.org/doi/10.1128/mra.01224-22 |
This study showed that high number of Novaseq 6000 reads mapped to Cowpea mild mottle virus isolate DSMZ PV-0090 using Geneious RNA mapper
|
|
|
Are you interested in mapping full-length transcripts? Yes/No
|
||
| Mapper | minimap2 | Summary |
| References | https://www.nature.com/articles/s41592-019-0617-2 |
minimap2 was used to map direct RNA and cDNA ONT reads to the human genome to identify plausible RNA isoforms
|
| https://www.nature.com/articles/s41598-020-70794-5 |
Minimap2 was used to map ONT and PacBio ROI cDNA reads to the virus genome to access the transcriptomic profile of the viral pathogen
|
|
| https://www.nature.com/articles/s41586-023-05896-x |
minimap2 in splice-aware mode was used to align PacBio to the Human GRCh38 genome to create a draft human pangenome
|
|
| https://www.nature.com/articles/s41467-020-15171-6 |
Nanopore reads were aligned to human hg38 genome in the spliced alignment mode with marked improvement in splice-site mapping
|
|
|
Are you interested in mapping full-length transcripts? No
|
||
| Mapper | Geneious RNA | Summary |
| References | https://www.cell.com/iscience/pdf/S2589-0042(23)00857-X.pdf |
Geneious RNA mapper was used to map ONT reads to the MERS-CoV genome to study the complex genome organization and expression network of MERS-CoV
|
|
Are you interested in mapping full-length transcripts? No
|
||
| Mapper | BBMap | Summary |
| References | https://academic.oup.com/bioinformatics/article/34/5/748/4562330 |
Evaluation of mappers for long read RNA-seq showed that BBMap, performed quite well with PacBio ROI reads and on simpler organisms with less multi-exonic genes.
|
|
Did you perform cDNA or Direct RNA sequencing? Direct RNA sequecing
|
||
| Mapper | minimap2 | Summary |
| References | https://www.nature.com/articles/s41592-022-01633-w |
This study align RNA strands generated by ONT software using minimap2 via Nanopolish to analyze cellular mRNA and noncoding RNA, and numerous RNA viruses
|
| https://www.nature.com/articles/s41592-019-0617-2 |
Minimap2 was used to map direct RNA and cDNA ONT reads to the human genome to identify plausible RNA isoforms
|
|
| https://www.nature.com/articles/s41598-020-70794-5 |
Minimap2 was used to map direct RNA and cDNA ONT reads to the virus genome to access the transcriptomic profile of the viral pathogen
|
|
| https://www.nature.com/articles/s41467-021-27393-3 |
Nanopore direct RNA sequencing reads were mapped using minimap2 to detect RNA modifications
|
|