The K-mer File Format: a standardized and compact disk representation of sets of k-mers.

SUMMARY: Bioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here, we introduce the K-mer File Format as a general lossless framework for storing and manipulating k-mer sets, realizing space savings of 3-5× compared to other formats, and bringing interoperability across tools. AVAILABILITY AND IMPLEMENTATION: Format specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Critical Assessment of Metagenome Interpretation: the second round of challenges.

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.

Cutevariant: a standalone GUI-based desktop application to explore genetic variations from an annotated VCF file.

Summary: Cutevariant is a graphical user interface (GUI)-based desktop application designed to filter variations from annotated VCF file. The application imports data into a local SQLite database where complex filter queries can be built either from GUI controllers or using a domain-specific language called Variant Query Language. Cutevariant provides more features than existing applications and is fully customizable thanks to a complete plugins architecture. Availability and implementation: Cutevariant is distributed as a multiplatform client-side software under an open source license and is available at https://github.com/labsquare/cutevariant.

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads.

Human genomes are typically assembled as consensus sequences that lack information on parental haplotypes. Here we describe a reference-free workflow for diploid de novo genome assembly that combines the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing1,2 with continuous long-read or high-fidelity3 sequencing data. Employing this strategy, we produced a completely phased de novo genome assembly for each haplotype of an individual of Puerto Rican descent (HG00733) in the absence of parental data. The assemblies are accurate (quality value > 40) and highly contiguous (contig N50 > 23 Mbp) with low switch error rates (0.17%), providing fully phased single-nucleotide variants, indels and structural variants. A comparison of Oxford Nanopore Technologies and Pacific Biosciences phased assemblies identified 154 regions that are preferential sites of contig breaks, irrespective of sequencing technology or phasing algorithms.

yacrd and fpa: upstream tools for long-read genome assembly.

MOTIVATION: Genome assembly is increasingly performed on long, uncorrected reads. Assembly quality may be degraded due to unfiltered chimeric reads; also, the storage of all read overlaps can take up to terabytes of disk space. RESULTS: We introduce two tools: yacrd for chimera removal and read scrubbing, and fpa for filtering out spurious overlaps. We show that yacrd results in higher-quality assemblies and is one hundred times faster than the best available alternative. AVAILABILITY AND IMPLEMENTATION: https://github.com/natir/yacrd and https://github.com/natir/fpa. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Graph analysis of fragmented long-read bacterial genome assemblies.

MOTIVATION: Long-read genome assembly tools are expected to reconstruct bacterial genomes nearly perfectly; however, they still produce fragmented assemblies in some cases. It would be beneficial to understand whether these cases are intrinsically impossible to resolve, or if assemblers are at fault, implying that genomes could be refined or even finished with little to no additional experimental cost. RESULTS: We propose a set of computational techniques to assist inspection of fragmented bacterial genome assemblies, through careful analysis of assembly graphs. By finding paths of overlapping raw reads between pairs of contigs, we recover potential short-range connections between contigs that were lost during the assembly process. We show that our procedure recovers 45% of missing contig adjacencies in fragmented Canu assemblies, on samples from the NCTC bacterial sequencing project. We also observe that a simple procedure based on enumerating weighted Hamiltonian cycles can suggest likely contig orderings. In our tests, the correct contig order is ranked first in half of the cases and within the top-three predictions in nearly all evaluated cases, providing a direction for finishing fragmented long-read assemblies. AVAILABILITY AND IMPLEMENTATION: https://gitlab.inria.fr/pmarijon/knot . SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.