ArticleBMC bioinformatics2021
SAUTE: sequence assembly using target enrichment.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Algorithm and Software to Type Stx Operons Accurately from Assembled Genomic Sequence.Microorganisms · 2026Article
- Breaking the culture habit: Complementing culture-based veterinary diagnostics with metagenomic data -A case study of feline and canine skin infections.BMC veterinary research · 2026Article
- Transition ofbioRxiv : the preprint server for biology · 2025Article
- 20 years later: unravelling the genomic success of New Zealand's home-grown AK3 community-associated methicillin-resistantMicrobial genomics · 2025Article
- Genomic epidemiology of strains currently and formerly classified as Enterobacter spp. recovered from equine necropsy samples.PloS one · 2025Article
- Indexing and searching petabase-scale nucleotide resources.Nature methods · 2024Article
- Genomic characterization of antimicrobial resistance in 61 aquatic bacterial isolates.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2024Article
- Metagenomic survey of antimicrobial resistance (AMR) in Maryland surface waters differentiated by high and low human impact.Microbiology resource announcements · 2024Article
- Identification and Characterization of tenMicroorganisms · 2023Article
- A discovery down under: decoding the draft genome sequence ofMicrobial genomics · 2023Article
- In Vitro Activity of Ceftolozane-Tazobactam againstAntibiotics (Basel, Switzerland) · 2023Article
- SAUTE: sequence assembly using target enrichment.BMC bioinformatics · 2021Article
- Characterization ofJournal of nematology · 2021Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundIllumina is the dominant sequencing technology at this time. Short length, short insert size, some systematic biases, and low-level carryover contamination in Illumina reads continue to make assembly of repeated regions a challenging problem. Some applications also require finding multiple well supported variants for assembled regions.
resultsTo facilitate assembly of repeat regions and to report multiple well supported variants when a user can provide target sequences to assist the assembly, we propose SAUTE and SAUTE_PROT assemblers. Both assemblers use de Bruijn graph on reads. Targets can be transcripts or proteins for RNA-seq reads and transcripts, proteins, or genomic regions for genomic reads. Target sequences are nucleotide and protein sequences for SAUTE and SAUTE_PROT, respectively.
conclusionsFor RNA-seq, comparisons with TRINITY, RNASPADES, SPALIGNER, and SPADES assembly of reads aligned to target proteins by DIAMOND show that SAUTE_PROT finds more coding sequences that translate to benchmark proteins. Using AMRFINDERPLUS calls, we find SAUTE has higher sensitivity and precision than SPADES, PLASMIDSPADES, SPALIGNER, and SPADES assembly of reads aligned to target regions by HISAT2. It also has better sensitivity than SKESA but worse precision.
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