Discover, rate, and verify biology preprints.

Unicycler: resolving bacterial genome assemblies from short and long sequencing reads

Unicycler scaffolds SPAdes short-read assembly graphs using long reads, producing more complete bacterial assemblies with fewer misassemblies than competing hybrid tools, even at low long-read depth.

The Sentieon Genomics Tools - A fast and accurate solution to variant calling from next-generation sequence data

Sentieon's rewrite of GATK and MuTect pipelines runs on average 36x faster than GATK Best Practices on public human data while matching its calls (average F-score 0.9996).

BugBase Predicts Organism Level Microbiome Phenotypes

BugBase assigns pathway coverage and traits (Gram stain, oxygen tolerance, pathogenicity) to individual taxa in 16S or shotgun microbiome data, detecting some functional differences bag-of-genes profiles miss.

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Canu's tf-idf weighted MinHash overlapping and error-filtered sparse overlap graph yield complete Nanopore microbial genomes and contig NG50 above 21 Mbp for PacBio human and Drosophila.

De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing

Base-by-base tests of raw nanopore current, native versus amplified DNA, detect 4mC, 5mC and 6mA without training data, recovering seven methylases' motifs (AUC 0.62–0.97).

STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq

Filtering STAR's chimeric alignments against gene annotations outscored 15 other fusion callers on 60 cancer cell lines and ran fastest, averaging 2.3 single-core hours per sample.

ATLAS: Analysis Tools for Low-depth and Ancient Samples

ATLAS, a C++ toolkit that models post-mortem damage when genotyping ancient or low-depth BAM data, avoided GATK's reference bias and made fewer errors at higher depth in simulations.

Mindboggling morphometry of human brains

Open source Mindboggle pipeline extracts cortical folds, sulci and fundi and computes diverse shape measures, yielding normative morphometry for 101 manually labeled healthy human brains.

Helical reconstruction in RELION

RELION 2.0 adds empirical Bayesian helical reconstruction with orientation priors, filament-level half-sets and local twist/rise optimisation, yielding near-atomic maps for four filament datasets.

Heterogeneity in polygenic scores for common human traits

Polygenic scores built 434 ways in Health and Retirement Study (HRS) participants varied widely in variance explained and inter-score correlation; European-derived weights underperformed in non-Hispanic Blacks.

Deep Recurrent Neural Network for Protein Function Prediction from Sequence

Bidirectional LSTMs read raw amino-acid sequence to call protein function without alignment; ten unannotated iron-sequestration candidates flagged in UniRef100 lowered free iron when expressed in E. coli.

Massively parallel digital transcriptional profiling of single cells

8-channel GemCode droplet barcoding captures ∼50% of loaded cells for 3′ mRNA counting, profiling 68k peripheral blood mononuclear cells and calling transplant chimerism from transcript variants.

DeepAD: Alzheimer’s Disease Classification via Deep Convolutional Neural Networks using MRI and fMRI

Caffe LeNet and GoogleNet trained on 2D slices from ADNI scans of adults over 75 report 98.84% to near-perfect accuracy, and 100% per subject for MRI after majority voting.

Gastruloids develop the three body axes in the absence of extraembryonic tissues and spatially localised signalling

Mouse embryonic stem cell aggregates (Gastruloids) form anteroposterior, dorsoventral and left-right axes without extraembryonic tissue or localised signals, through Nodal-initiated, Wnt-stabilised T/Brachyury polarisation.

Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade

Immunogenomic profiling of 8243 TCGA samples across 20 solid cancers yields an immune atlas and a random-forest-derived immunophenoscore stratifying melanoma responders to checkpoint blockade.

Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men

yHaplo walks the Y-chromosome tree with an error-tolerant breadth-first search, labelling the 1,244 1000 Genomes males in 20 seconds and matching every gold-standard call.

WhatsHap: fast and accurate read-based phasing

Re-aligning reads to both alleles gives WhatsHap the lowest PacBio switch error rates (full coverage: 0.24% real, 0.02% simulated) and better indel phasing than hapCUT and phASER.

Automating Morphological Profiling with Generic Deep Convolutional Networks

ImageNet-pretrained Inception-v3, without fine-tuning or segmentation, reaches 91% mechanism-of-action accuracy on illumination-corrected BBBC021 versus 90% for classical mean profiles, running in 22 minutes versus over 10 hours for single-core CellProfiler.

UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing

Quality-score-free UNOISE2 clusters unique Illumina amplicon reads by abundance skew and edit distance with two preset parameters, matching or exceeding DADA2 accuracy on 16S mock communities.

SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development

Unsupervised trajectory inference by SCORPIUS outperformed Wanderlust, Monocle and Waterfall across ten scRNA-seq datasets and predicted falling protein synthesis during dendritic cell development, validated in vivo.