Improved sub-genomic RNA prediction with the ARTIC protocol.

Viral subgenomic RNA (sgRNA) plays a major role in SARS-COV2's replication, pathogenicity, and evolution. Recent sequencing protocols, such as the ARTIC protocol, have been established. However, due to the viral-specific biological processes, analyzing sgRNA through viral-specific read sequencing data is a computational challenge.

Designing efficient randstrobes for sequence similarity analyses.

Motivation: Substrings of length k, commonly referred to as k-mers, play a vital role in sequence analysis. However, k-mers are limited to exact matches between sequences leading to alternative constructs. We recently introduced a class of new constructs, strobemers, that can match across substitutions and smaller insertions and deletions.

Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.

Y chromosomal ampliconic genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been studied in great apes; however, the diversity of splicing variants remains unexplored. Here, we deciphered the sequences of polyadenylated transcripts of all nine YAG families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan).

Nanopore sequencing of PCR products enables multicopy gene family reconstruction.

The importance of gene amplifications in evolution is more and more recognized. Yet, tools to study multi-copy gene families are still scarce, and many such families are overlooked using common sequencing methods. Haplotype reconstruction is even harder for polymorphic multi-copy gene families.

Efficient mapping of accurate long reads in minimizer space with mapquik.

DNA sequencing data continue to progress toward longer reads with increasingly lower sequencing error rates. We focus on the critical problem of mapping, or aligning, low-divergence sequences from long reads (e.g.

isONform: reference-free transcriptome reconstruction from Oxford Nanopore data.

Motivation: With advances in long-read transcriptome sequencing, we can now fully sequence transcripts, which greatly improves our ability to study transcription processes. A popular long-read transcriptome sequencing technique is Oxford Nanopore Technologies (ONT), which through its cost-effective sequencing and high throughput, has the potential to characterize the transcriptome in a cell. However, due to transcript variability and sequencing errors, long cDNA reads need substantial bioinformatic processing to produce a set of isoform predictions from the reads.

A survey of mapping algorithms in the long-reads era.

It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend framework used for short reads to a seed-and-chain framework due to the seed abundance in each read. The main novelties are based on alternative seed constructs or chaining formulations.

Entropy predicts sensitivity of pseudorandom seeds.

Seed design is important for sequence similarity search applications such as read mapping and average nucleotide identity (ANI) estimation. Although -mers and spaced -mers are likely the most well-known and used seeds, sensitivity suffers at high error rates, particularly when indels are present. Recently, we developed a pseudorandom seeding construct, strobemers, which was empirically shown to have high sensitivity also at high indel rates.

Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.

Y-chromosomal Ampliconic Genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been recently studied in great apes, however, the diversity of splicing variants remains unexplored. Here we deciphered the sequences of polyadenylated transcripts of all nine YAG families (, , , , , , , , and ) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan).

Strobealign: flexible seed size enables ultra-fast and accurate read alignment.

Read alignment is often the computational bottleneck in analyses. Recently, several advances have been made on seeding methods for fast sequence comparison. We combine two such methods, syncmers and strobemers, in a novel seeding approach for constructing dynamic-sized fuzzy seeds and implement the method in a short-read aligner, strobealign.

Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment.

In many parts of the world, human-mediated environmental change is depleting biodiversity faster than it can be characterized, while invasive species cause agricultural damage, threaten human health and disrupt native habitats. Consequently, the application of effective approaches for rapid surveillance and identification of biological specimens is increasingly important to inform conservation and biosurveillance efforts. Taxonomic assignments have been greatly advanced using sequence-based applications, such as DNA barcoding, a diagnostic technique that utilizes PCR and DNA sequence analysis of standardized genetic regions.

Safety in Multi-Assembly via Paths Appearing in All Path Covers of a DAG.

A multi-assembly problem asks to reconstruct multiple genomic sequences from mixed reads sequenced from all of them. Standard formulations of such problems model a solution as a path cover in a directed acyclic graph, namely a set of paths that together cover all vertices of the graph. Since multi-assembly problems admit multiple solutions in practice, we consider an approach commonly used in standard genome assembly: output only partial solutions (contigs, or safe paths), that appear in all path cover solutions.

Effective sequence similarity detection with strobemers.

-mer-based methods are widely used in bioinformatics for various types of sequence comparisons. However, a single mutation will mutate consecutive -mers and make most -mer-based applications for sequence comparison sensitive to variable mutation rates. Many techniques have been studied to overcome this sensitivity, for example, spaced -mers and -mer permutation techniques, but these techniques do not handle indels well.

Accurate spliced alignment of long RNA sequencing reads.

Motivation: Long-read RNA sequencing technologies are establishing themselves as the primary techniques to detect novel isoforms, and many such analyses are dependent on read alignments. However, the error rate and sequencing length of the reads create new challenges for accurately aligning them, particularly around small exons.

Results: We present an alignment method uLTRA for long RNA sequencing reads based on a novel two-pass collinear chaining algorithm.

NGSpeciesID: DNA barcode and amplicon consensus generation from long-read sequencing data.

Third-generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long-read sequences. This is not only advantageous for genome sequencing projects, but also advantageous for amplicon-based high-throughput sequencing experiments, such as DNA barcoding.

Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis.

Oxford Nanopore (ONT) is a leading long-read technology which has been revolutionizing transcriptome analysis through its capacity to sequence the majority of transcripts from end-to-end. This has greatly increased our ability to study the diversity of transcription mechanisms such as transcription initiation, termination, and alternative splicing. However, ONT still suffers from high error rates which have thus far limited its scope to reference-based analyses.

DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies.

Background: Although the Y chromosome plays an important role in male sex determination and fertility, it is currently understudied due to its haploid and repetitive nature. Methods to isolate Y-specific contigs from a whole-genome assembly broadly fall into two categories. The first involves retrieving Y-contigs using proportion sharing with a female, but such a strategy is prone to false positives in the absence of a high-quality, complete female reference.

Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon.

A significant portion of genes in vertebrate genomes belongs to multigene families, with each family containing several gene copies whose presence/absence, as well as isoform structure, can be highly variable across individuals. Existing de novo techniques for assaying the sequences of such highly-similar gene families fall short of reconstructing end-to-end transcripts with nucleotide-level precision or assigning alternatively spliced transcripts to their respective gene copies. We present IsoCon, a high-precision method using long PacBio Iso-Seq reads to tackle this challenge.

Structural Variation Detection with Read Pair Information: An Improved Null Hypothesis Reduces Bias.

Reads from paired-end and mate-pair libraries are often utilized to find structural variation in genomes, and one common approach is to use their fragment length for detection. After aligning read pairs to the reference, read pair distances are analyzed for statistically significant deviations. However, previously proposed methods are based on a simplified model of observed fragment lengths that does not agree with data.

Assembly scaffolding with PE-contaminated mate-pair libraries.

Motivation: Scaffolding is often an essential step in a genome assembly process, in which contigs are ordered and oriented using read pairs from a combination of paired-end libraries and longer-range mate-pair libraries. Although a simple idea, scaffolding is unfortunately hard to get right in practice. One source of problems is so-called PE-contamination in mate-pair libraries, in which a non-negligible fraction of the read pairs get the wrong orientation and a much smaller insert size than what is expected.

Gap Filling as Exact Path Length Problem.

One of the last steps in a genome assembly project is filling the gaps between consecutive contigs in the scaffolds. This problem can be naturally stated as finding an s-t path in a directed graph whose sum of arc costs belongs to a given range (the estimate on the gap length). Here s and t are any two contigs flanking a gap.

BESST--efficient scaffolding of large fragmented assemblies.

Background: The use of short reads from High Throughput Sequencing (HTS) techniques is now commonplace in de novo assembly. Yet, obtaining contiguous assemblies from short reads is challenging, thus making scaffolding an important step in the assembly pipeline. Different algorithms have been proposed but many of them use the number of read pairs supporting a linking of two contigs as an indicator of reliability.

The Norway spruce genome sequence and conifer genome evolution.

Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage.