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Javier Santoyo@jsantoyo
18 Sep 2025
UMI-nea: A Fast, Robust Tool for Reference-Free UMI Deduplication and Accurate Quantification. #UMIdeduplication #ReferenceFree #Bioinformatics #Genomics academic.oup.com/bioinformat…
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1,362
Javier Santoyo@jsantoyo
29 Jun 2025
The reference-free pangenome of Arabidopsis thaliana. #ArabidopsisGenomes #Pangenome #ReferenceFree #Genomics #Bioinformatics @biorxiv_bioinfo @edgenome biorxiv.org/content/10.1101/…
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Javier Santoyo@jsantoyo
23 Oct 2023
PanKmer: k-mer based and reference-free pangenome analysis. #Pangenomes #kmers #ReferenceFree #Bioinformatics academic.oup.com/bioinformat…

PanKmer: k-mer-based and reference-free pangenome analysis

AbstractSummary. Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome an

academic.oup.com
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4,744
Javier Santoyo@jsantoyo
2 Apr 2023
PanKmer: k-mer based and reference-free pangenome analysis. #Kmer #ReferenceFree #Pangenome biorxiv.org/content/10.1101/…

PanKmer: k-mer based and reference-free pangenome analysis

Summary Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages graph-based methods...

biorxiv.org
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4,376
Eduardo Eyras@EduEyras
11 Jul 2022
Very happy to see RATTLE published genomebiology.biomedcentral.… #RATTLE #referencefree #transcriptomics #longreads #RNA #Nanopore

RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing

Genome Biology - Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes. Current methods for transcript identification and quantification rely on mapping reads to a...

link.springer.com
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Javier Santoyo@jsantoyo
22 Oct 2021
Comparability of reference-based and reference-free transcriptome analysis approaches at the gene expression level. #TranscriptomeAnalysis #ReferenceFree #ReferenceBased bmcbioinformatics.biomedcent… @BMCBioinfo

Comparability of reference-based and reference-free transcriptome analysis approaches at the gene...

BMC Bioinformatics - Lately, high-throughput RNA sequencing has been extensively used to elucidate the transcriptome landscape and dynamics of cell types of different species. In particular, for...

link.springer.com
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Javier Santoyo@jsantoyo
11 Jun 2021
NanoSpring: reference-free lossless compression of nanopore sequencing reads using an approximate assembly approach. @nanopore #SequencingReads #LosslessCompression #ReferenceFree biorxiv.org/content/10.1101/…
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Eduardo Eyras@EduEyras
9 Feb 2020
Reference-free reconstruction and quantification of transcriptomes from long-read sequencing biorxiv.org/content/10.1101/… #transcriptomics #referencefree #denovo #nanopore

Reference-free reconstruction and quantification of transcriptomes from long-read sequencing

Single-molecule long-read sequencing provides an unprecedented opportunity to measure the transcriptome from any sample [1][1]–[3][2]. However, current methods for the analysis of transcriptomes from...

biorxiv.org
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Nick Wong AU/MEL@methylnick
9 Dec 2019
Yes!!! Using @lexogen to benchmark and sanity check the tool. @EduEyras #RATTLE @nanopore #referenceFree @abacbs #ABACBSGIW19 @MonashBioinfo
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