Motivation An important step in the transcriptomic analysis of individual cells involves manually determining the cellular identities. To ease this labor-intensive annotation of cell-types, there has been a growing interest in automated cell annotation, which can be achieved by training classification algorithms on previously annotated datasets. Existing pipelines employ dataset integration methods to remove potential batch effects between source (annotated) and target (unannotated) datasets. However, the integration and classification steps are usually independent of each other and performed by different tools. We propose JIND (joint integration and discrimination for automated single-cell annotation), a neural-network-based framework for automated cell-type identification that performs integration in a space suitably chosen to facilitate cell classification. To account for batch effects, JIND performs a novel asymmetric alignment in which unseen cells are mapped onto the previously learned latent space, avoiding the need of retraining the classification model for new datasets. JIND also learns cell-type-specific confidence thresholds to identify cells that cannot be reliably classified. Results We show on several batched datasets that the joint approach to integration and classification of JIND outperforms in accuracy existing pipelines, and a smaller fraction of cells is rejected as unlabeled as a result of the cell-specific confidence thresholds. Moreover, we investigate cells misclassified by JIND and provide evidence suggesting that they could be due to outliers in the annotated datasets or errors in the original approach used for annotation of the target batch.

Single-cell RNA-Sequencing has the potential to provide deep biological insights by revealing complex regulatory interactions across diverse cell phenotypes at single-cell resolution. However, current single-cell gene regulatory network inference methods produce a single regulatory network per input dataset, limiting their capability to uncover complex regulatory relationships across related cell phenotypes. We present SimiC, a single-cell gene regulatory inference framework that overcomes this limitation by jointly inferring distinct, but related, gene regulatory dynamics per phenotype. We show that SimiC uncovers key regulatory dynamics missed by previously proposed methods across a range of systems, both model and non-model alike. In particular, SimiC was able to uncover CAR T cell dynamics after tumor recognition and key regulatory patterns on a regenerating liver, and was able to implicate glial cells in the generation of distinct behavioral states in honeybees. SimiC hence establishes a new approach to quantitating regulatory architectures between distinct cellular phenotypes, with far-reaching implications for systems biology.

Unsupervised ensemble learning refers to methods devised for a particular task that combine data pro-vided by decision learners taking into account their reliability, which is usually inferred from the data. Here, the variant calling step of the next generation sequencing technologies is formulated as an unsuper-vised ensemble classification problem. A variant calling algorithm based on the expectation-maximization algorithm is further proposed that estimates the maximum-a-posteriori decision among a number of classes larger than the number of different labels provided by the learners. Experimental results with real human DNA sequencing data show that the proposed algorithm is competitive compared to state-of -the-art variant callers as GATK, HTSLIB, and Platypus.(c) 2022 The Author(s). Published by Elsevier Ltd.This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )

Intra-tumor heterogeneity renders the identification of somatic single-nucleotide variants (SNVs) a challenging problem. In particular, low-frequency SNVs are hard to distinguish from sequencing artifacts. While the increasing availability of multi-sample tumor DNA sequencing data holds the potential for more accurate variant calling, there is a lack of high-sensitivity multi-sample SNV callers that utilize these data. Here we report Moss, a method to identify low-frequency SNVs that recur in multiple sequencing samples from the same tumor. Moss provides any existing single-sample SNV caller the ability to support multiple samples with little additional time overhead. We demonstrate that Moss improves recall while maintaining high precision in a simulated dataset. On multi-sample hepatocellular carcinoma, acute myeloid leukemia and colorectal cancer datasets, Moss identifies new low-frequency variants that meet manual review criteria and are consistent with the tumor's mutational signature profile. In addition, Moss detects the presence of variants in more samples of the same tumor than reported by the single-sample caller. Moss' improved sensitivity in SNV calling will enable more detailed downstream analyses in cancer genomics. The study of tumour heterogeneity can be improved by sequencing multiple samples, but currently available variant callers have not been tailored to integrate them. Here the authors present Moss, a tool that can leverage multiple samples to improve somatic variant calling in different cancers.

Motivation: Nanopore sequencing technologies are rapidly gaining popularity, in part, due to the massive amounts of genomic data they produce in short periods of time (up to 8.5 TB of data in <72 h). To reduce the costs of transmission and storage, efficient compression methods for this type of data are needed. Results: We introduce RENANO, a reference-based lossless data compressor specifically tailored to FASTQ files generated with nanopore sequencing technologies. RENANO improves on its predecessor ENANO, currently the state of the art, by providing a more efficient base call sequence compression component. Two compression algorithms are introduced, corresponding to the following scenarios: (1) a reference genome is available without cost to both the compressor and the decompressor and (2) the reference genome is available only on the compressor side, and a compacted version of the reference is included in the compressed file. We compare the compression performance of RENANO against ENANO on several publicly available nanopore datasets. RENANO improves the base call sequences compression of ENANO by 39.8% in scenario (1), and by 33.5% in scenario (2), on average, over all the datasets. As for total file compression, the average improvements are 12.7% and 10.6%, respectively. We also show that RENANO consistently outperforms the recent general-purpose genomic compressor Genozip.

Motivation: Mass spectrometry (MS) data, used for proteomics and metabolomics analyses, have seen considerable growth in the last years. Aiming at reducing the associated storage costs, dedicated compression algorithms for MS data have been proposed, such as MassComp and MSNumpress. However, these algorithms focus on either lossless or lossy compression, respectively, and do not exploit the additional redundancy existing across scans contained in a single file. We introduce mspack, a compression algorithm for MS data that exploits this additional redundancy and that supports both lossless and lossy compression, as well as the mzML and the legacy mzXML formats. mspack applies several preprocessing lossless transforms and optional lossy transforms with a configurable error, followed by the general purpose compressors gzip or bsc to achieve a higher compression ratio. Results: We tested mspack on several datasets generated by commonly used MS instruments. When used with the bsc compression backend, mspack achieves on average 76% smaller file sizes for lossless compression and 94% smaller file sizes for lossy compression, as compared with the original files. Lossless mspack achieves 10-60% lower file sizes than MassComp, and lossy mspack compresses 36-60% better than the lossy MSNumpress, for the same error, while exhibiting comparable accuracy and running time. Supplementary information: Supplementary data are available at Bioinformatics online.

Motivation: The amount of genomic data generated globally is seeing explosive growth, leading to increasing needs for processing, storage and transmission resources, which motivates the development of efficient compression tools for these data. Work so far has focused mainly on the compression of data generated by short-read technologies. However, nanopore sequencing technologies are rapidly gaining popularity due to the advantages offered by the large increase in the average size of the produced reads, the reduction in their cost and the portability of the sequencing technology. We present ENANO (Encoder for NANOpore), a novel lossless compression algorithm especially designed for nanopore sequencing FASTQ files. Results: The main focus of ENANO is on the compression of the quality scores, as they dominate the size of the compressed file. ENANO offers two modes, Maximum Compression and Fast (default), which trade-off compression efficiency and speed. We tested ENANO, the current state-of-the-art compressor SPRING and the general compressor pigz on several publicly available nanopore datasets. The results show that the proposed algorithm consistently achieves the best compression performance (in both modes) on every considered nanopore dataset, with an average improvement over pigz and SPRING of >24.7% and 6.3%, respectively. In addition, in terms of encoding and decoding speeds, ENANO is 2.9x and 1.7x times faster than SPRING, respectively, with memory consumption up to 0.2 GB.

MOTIVATION: In an effort to provide a response to the ever-expanding generation of genomic data, the International Organization for Standardization (ISO) is designing a new solution for the representation, compression and management of genomic sequencing data: the MPEG-G standard. This paper discusses the first implementation of an MPEG-G compliant entropy codec: GABAC. GABAC combines proven coding technologies, such as context-adaptive binary arithmetic coding, binarization schemes and transformations, into a straightforward solution for the compression of sequencing data. RESULTS: We demonstrate that GABAC outperforms well-established (entropy) codecs in a significant set of cases and thus can serve as an extension for existing genomic compression solutions, such as CRAM. AVAILABILITY: The GABAC library is written in C++. We also provide a command line application which exercises all features provided by the library. GABAC can be downloaded from https://github.com/mitogen/gabac. SUPPLEMENTARY INFORMATION: Supplementary data, including a complete list of the funding mechanisms and acknowledgements, are available at Bioinformatics online.

Motivation: Sequencing data are often summarized at different annotation levels for further analysis, generally using the general feature format (GFF) or its descendants, gene transfer format (GTF) and GFF3. Existing utilities for accessing these files, like gffutils and gffread, do not focus on reducing the storage space, significantly increasing it in some cases. We propose GPress, a framework for querying GFF files in a compressed form. GPress can also incorporate and compress expression files from both bulk and single-cell RNA-Seq experiments, supporting simultaneous queries on both the GFF and expression files. In brief, GPress applies transformations to the data which are then compressed with the general lossless compressor BSC. To support queries, GPress compresses the data in blocks and creates several index tables for fast retrieval. Results: We tested GPress on several GFF files of different organisms, and showed that it achieves on average a 61% reduction in size with respect to gzip (the current de facto compressor for GFF files) while being able to retrieve all annotations for a given identifier or a range of coordinates in a few seconds (when run in a common laptop). In contrast, gffutils provides faster retrieval but doubles the size of the GFF files. When additionally linking an expression file, we show that GPress can reduce its size by more than 68% when compared to gzip (for both bulk and single-cell RNA-Seq experiments), while still retrieving the information within seconds. Finally, applying BSC to the data streams generated by GPress instead of to the original file shows a size reduction of more than 44% on average.

MOTIVATION: Variants identified by current genomic analysis pipelines contain many incorrectly called variants. These can be potentially eliminated by applying state-of-the-art filtering tools, such as Variant Quality Score Recalibration (VQSR) or Hard Filtering (HF). However, these methods are very user-dependent and fail to run in some cases. We propose VEF, a variant filtering tool based on decision tree ensemble methods that overcomes the main drawbacks of VQSR and HF. Contrary to these methods, we treat filtering as a supervised learning problem, using variant call data with known "true" variants, i.e., gold standard, for training. Once trained, VEF can be directly applied to filter the variants contained in a given VCF file (we consider training and testing VCF files generated with the same tools, as we assume they will share feature characteristics). RESULTS: For the analysis, we used Whole Genome Sequencing (WGS) Human datasets for which the gold standards are available. We show on these data that the proposed filtering tool VEF consistently outperforms VQSR and HF. In addition, we show that VEF generalizes well even when some features have missing values, when the training and testing datasets differ in coverage, and when sequencing pipelines other than GATK are used. Finally, since the training needs to be performed only once, there is a significant saving in running time when compared to VQSR (4 versus 50minutes approximately for filtering the SNPs of a WGS Human