Sand Martin Genome Assembly and Multi-Method Gene Annotations

Genome and genome annotation of Riparia riparia (sand martin). The dataset includes a masked genome assembly, transcriptome assembly, and gene annotations generated using four distinct methods: GeMoMa, Helixer, StringTie, and EVidenceModeler. It was published by Miroslav Nuriddinov in April 2026.

Use Cases

• Compare gene structure predictions from the homology-based GeMoMa.gff, ab initio Helixer.gff, and RNA-seq derived StringTie.gtf annotations.
• Identify repetitive genomic elements using the RepeatMasker.bed file and analyze their distribution with the repeats.statistic.tsv.
• Use the combined EVidenceModeler.gff3 annotation as a consensus gene set for downstream functional or evolutionary analyses.
• Assemble transcripts or map sequencing reads using the provided trinity_expressed_longest_iso.fasta transcriptome and riRi.soma-enhanced.both.rf_p2.fa genome assembly.

Strengths

• Provides four complementary gene annotation sets (GeMoMa, Helixer, StringTie, EVM) for a single genome, enabling method comparison.
• Includes both raw (riRi.soma-enhanced.both.rf_p2.fa) and repeat-masked (riRi.soma-enhanced.both.rf_p2.masked.fa) genome assemblies.
• Dataset is 1.9 GB, indicating a complete genome-scale resource.

Limitations

• The number of annotated genes, contigs, or assembly statistics are not provided in the description.
• Annotations are specific to a single bird species (Riparia riparia), limiting broad taxonomic comparisons without additional data.
• Lacks explicit validation metrics for the accuracy of the different gene prediction methods.

Provenance

Source

Miroslav Nuriddinov via figshare.

Collection Method

Genome assembly enhanced with somatic data, with annotations generated via homology (GeMoMa), ab initio prediction (Helixer), RNA-seq alignment (StringTie), and evidence integration (EVM).

Freshness

Last updated in April 2026.