ARGminer
Curation of antibiotic resistance gene (ARG) databases is a labor-intensive process that requires expert knowledge to manually collect, correct, and/or annotate individual genes. Correspondingly, updates to existing databases tend to be infrequent, commonly requiring years for completion and often containing inconsistences. Further, because of limitations of manual curation, most existing ARG databases contain only a small proportion of known ARGs (~5k genes). A new approach is needed to achieve a truly comprehensive ARG database, while also maintaining a high level of accuracy. Here we propose a new web-based curation system, ARG-miner, which supports annotation of ARGs at multiple levels, including: gene name, antibiotic category, resistance mechanism, and evidence for mobility and occurrence in clinically-important bacterial strains. To overcome limitations of manual curation, we employ crowdsourcing as a novel strategy for expanding curation capacity towards achieving a truly comprehensive, up-to-date database. We develop and validate the approach by comparing performance of multiple cohorts of curators with varying levels of expertise, demonstrating that ARG-miner is more cost effective and less time-consuming relative to traditional expert curation. We further demonstrate the reliability of a trust validation filter for rejecting confounding input generated by spammers. Crowdsourcing was found to be as accurate as expert annotation, with an accuracy >90% for the annotation of a diverse test set of ARGs. ARG-miner provides a public API and database available here.
DeepMicro
Human microbiota plays a key role in human health and growing evidence supports the potential use of microbiome as a predictor of various diseases. However, the high-dimensionality of microbiome data, often in the order of hundreds of thousands, yet low sample sizes, poses great challenge for machine learning-based prediction algorithms. This imbalance induces the data to be highly sparse, preventing from learning a better prediction model. Also, there has been little work on deep learning applications to microbiome data with a rigorous evaluation scheme. To address these challenges, we propose DeepMicro, a deep representation learning framework allowing for an effective representation of microbiome profiles. DeepMicro successfully transforms high-dimensional microbiome data into a robust low-dimensional representation using various autoencoders and applies machine learning classification algorithms on the learned representation. In disease prediction, DeepMicro outperforms the current best approaches based on the strain-level marker profile in five different datasets. In addition, by significantly reducing the dimensionality of the marker profile, DeepMicro accelerates the model training and hyperparameter optimization procedure with 8X–30X speedup over the basic approach. DeepMicro is freely available here.
NanoARG
Direct and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effective environmental monitoring tools should ideally capture not only antibiotic resistance genes (ARGs), but also mobile genetic elements (MGEs) and indicators of co-selective forces, such as metal resistance genes (MRGs). A major challenge towards characterizing the potential human health risk of antibiotic resistance is the ability to identify ARG-carrying microorganisms, of which human pathogens are arguably of greatest risk. Historically, short reads produced by next-generation sequencing technologies have hampered confidence in assemblies for achieving these purposes. Here, we introduce NanoARG, an online computational resource that takes advantage of the long reads produced by nanopore sequencing technology. Specifically, long nanopore reads enable identification of ARGs in the context of relevant neighboring genes, thus providing valuable insight into mobility, co-selection, and pathogenicity. NanoARG was applied to study a variety of nanopore sequencing data to demonstrate its functionality. NanoARG was further validated through characterizing its ability to correctly identify ARGs in sequences of varying lengths and a range of sequencing error rates. NanoARG allows users to upload sequence data online and provides various means to analyze and visualize the data, including quantitative and simultaneous profiling of ARGs, MRGs, MGEs, and putative pathogens. A user-friendly interface allows users the analysis of long DNA sequences (including assembled contigs), facilitating data processing, analysis, and visualization. NanoARG is publicly available and freely accessible here.
MetaCompare
The spread of antibiotic resistance is a growing public health concern. While numerous studies have highlighted the importance of environmental sources and pathways of the spread of antibiotic resistance, a systematic means of comparing and prioritizing risks represented by various environmental compartments is lacking. Here, we introduce MetaCompare, a publicly available tool for ranking "resistome risk", which we define as the potential for antibiotic resistance genes (ARGs) to be associated with mobile genetic elements (MGEs) and mobilize to pathogens based on metagenomic data. A computational pipeline was developed in which each ARG is evaluated based on relative abundance, mobility, and presence within a pathogen. This is determined through the assembly of shotgun sequencing data and analysis of contigs containing ARGs to determine if they contain sequence similarity to MGEs or human pathogens. Based on the assembled metagenomes, samples are projected into a 3-dimensional hazard space and assigned resistome risk scores. To validate, we tested previously published metagenomic data derived from distinct aquatic environments. Based on unsupervised machine learning, the test samples clustered in the hazard space in a manner consistent with their origin. The derived scores produced a well-resolved ascending resistome risk ranking of: wastewater treatment plant effluent, dairy lagoon, and hospital sewage.
BisPin and BFAST-Gap
BisPin is a new multiprocess bisulfite-treated short DNA read mapper written in Python 2.7. It performs alignments using BFAST, leveraging its multithreading functionality and thorough hash-based indexing strategy. BisPin is feature rich and supports directional, nondirectional, PBAT, and hairpin construction strategies. BisPin approaches read mapping by converting the Cs to Ts and the Gs to As in both the reads and the reference genome. BisPin uses fast rescoring to disambiguate ambiguously aligned reads for a superior amount of uniquely mapped reads compared to other mappers. The performance of BisPin was evaluated on both real and simulated data in comparison to other read mappers. BFAST-Gap is a modified version of BFAST meant for Ion Torrent reads. It uses a parameterized logistic function to determine the weights of the gap open and extension penalties based on the homopolymer run length of the DNA read. This is because the Ion Torrent sequencing technology can overcall and undercall homopolymer runs. BisPin works with both BFAST-Gap and BFAST. BFAST-Gap is compatible with indexes built with BFAST. There are few mappers that specifically address Ion Torrent data. BFAST-Gap works with Illumina reads as well. Results: BisPin with BFAST consistently had a higher amount of uniquely mapped reads compared to other mappers on real data using a variety of construction strategies. Using a hairpin validation strategy, BisPin was superior using the maximum score, and it mapped 73% of reads correctly. BisPin with BFAST-Gap on Ion Torrent reads with a logistic gap open penalty function improved mapping accuracy with real and simulated data. On simulated bisulfite Ion Torrent data, the area under the curve was improved by approximately seven, and on one real data set, the uniquely mapped percent was improved by seven percent. BFAST-Gap performed better than TMAP on simulated regular Ion Torrent reads, and TMAP is designed for Ion Torrent reads. Other read mappers had worse performance. Conclusions: BisPin and BFAST-Gap have consistently good accuracy with a variety of data. BisPin is feature-rich. This makes BisPin and BFAST-Gap useful additions to read mapping software.
DeepARG
Growing concerns about increasing rates of antibiotic resistance call for expanded and comprehensive global monitoring. Advancing methods for monitoring of environmental media (e.g., wastewater, agricultural waste, food, and water) is especially needed for identifying potential resources of novel antibiotic resistance genes (ARGs), hot spots for gene exchange, and as pathways for the spread of ARGs and human exposure. Next-generation sequencing now enables direct access and profiling of the total metagenomic DNA pool, where ARGs are typically identified or predicted based on the “best hits” of sequence searches against existing databases. Unfortunately, this approach produces a high rate of false negatives. To address such limitations, we propose here a deep learning approach, taking into account a dissimilarity matrix created using all known categories of ARGs. Two deep learning models, DeepARG-SS and DeepARG-LS, were constructed for short read sequences and full gene length sequences, respectively. Evaluation of the deep learning models over 30 antibiotic resistance categories demonstrates that the DeepARG models can predict ARGs with both high precision (>0.97) and recall (>0.90). The models displayed an advantage over the typical best hit approach, yielding consistently lower false negative rates and thus higher overall recall (>0.90). As more data become available for under-represented ARG categories, the DeepARG models’ performance can be expected to be further enhanced due to the nature of the underlying neural networks. Our newly developed ARG database, DeepARG-DB, encompasses ARGs predicted with a high degree of confidence and extensive manual inspection, greatly expanding current ARG repositories. The deep learning models developed here offer more accurate antimicrobial resistance annotation relative to current bioinformatics practice. DeepARG does not require strict cutoffs, which enables identification of a much broader diversity of ARGs. The DeepARG models and database are available as a command line version and as a Web service here.
FastViromeExplorer
With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.
InfoTrim
Biological DNA reads are often trimmed before mapping, genome assembly, and other tasks to improve the quality of the results. Biological sequence complexity relates to alignment quality as low complexity regions can align poorly. There are many read trimmers, but many do not use sequence complexity for trimming. Alignment of reads generated from whole genome bisulfite sequencing is especially challenging since bisulfite treated reads tend to reduce sequence complexity. InfoTrim, a new read trimmer, was created to explore these issues. It is evaluated against five other trimmers using four read mappers on real and simulated bisulfite treated DNA data. InfoTrim has reasonable results that are consistent with other read mappers.
UPS-indel
Indels, though differing in allele sequence and position, are biologically equivalent when they lead to the same altered sequences. Storing biologically equivalent indels as distinct entries in databases causes data redundancy, and may mislead downstream analysis and interpretations. About 10% of the human indels stored in dbSNP are redundant. It is thus desirable to have a unified system for identifying and representing equivalent indels in publically available databases. Moreover, a unified system is also desirable to compare the indel calling results produced by different tools. This paper describes UPS-indel, a utility tool that creates a universal positioning system for indels so that equivalent indels can be uniquely determined by their coordinates in the new system, which also can be used to compare indel calling results produced by different tools. UPS-indel identifies nearly 15% indels in dbSNP (version 142) as redundant across all human chromosomes, higher than previously reported. When applied to COSMIC coding and noncoding indel datasets, UPS-indel identifies nearly 29% and 13% indels as redundant, respectively. Comparing the performance of UPS-indel with existing variant normalization tools vt normalize, BCFtools, and GATK LeftAlignAndTrimVariants shows that UPS-indel is able to identify 456,352 more redundant indels in dbSNP; 2,118 more in COSMIC coding, and 553 more in COSMIC noncoding indel dataset in addition to the ones reported jointly by these tools. Moreover, comparing UPS-indel to other state-of-the-art approaches for indel call set comparison demonstrates that UPS-indel is clearly superior to other approaches in finding indels in common among call sets. UPS-indel is theoretically proven to find all equivalent indels, and is thus exhaustive. UPS-indel is written in C++ and the command line version is freely available here. The online version of UPS-indel is available here.
MetaStorm
Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm, which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution.
BAM-ABS
DNA methylation is an epigenetic modification critical for normal development and diseases. The determination of genome-wide DNA methylation at single-nucleotide resolution is made possible by sequencing bisulfite treated DNA with next generation high-throughput sequencing. However, aligning bisulfite short reads to a reference genome remains challenging as only a limited proportion of them (around 50–70%) can be aligned uniquely; a significant proportion, known as multireads, are mapped to multiple locations and thus discarded from downstream analyses, causing financial waste and biased methylation inference. To address this issue, we develop a Bayesian model that assigns multireads to their most likely locations based on the posterior probability derived from information hidden in uniquely aligned reads. Analyses of both simulated data and real hairpin bisulfite sequencing data show that our method can effectively assign approximately 70% of the multireads to their best locations with up to 90% accuracy, leading to a significant increase in the overall mapping efficiency. Moreover, the assignment model shows robust performance with low coverage depth, making it particularly attractive considering the prohibitive cost of bisulfite sequencing. Additionally, results show that longer reads help improve the performance of the assignment model. The assignment model is also robust to varying degrees of methylation and varying sequencing error rates. Finally, incorporating prior knowledge on mutation rate and context specific methylation level into the assignment model increases inference accuracy. The assignment model is implemented in the BAM-ABS package and freely available here.
HMMvar and HMMvar-multi
Small indels account for the second largest portion of human variants, however, available methods for indel functional predictions, no matter in coding or noncoding regions, are many fewer compared to those for SNPs. We developed HMMvar for predicting the functional effects of both SNPs and indels in coding regions of sequences.
Complex diseases are likely to be caused by multiple genes and/or multiple mutations on individual genes, so quantitively measuring the effect of multiple variants together should be helpful for detecting causal genes/mutations for diseases. HMMvar-multi predicts the functional effects of multiple variants in the same gene based on HMMvar.
HMMvar-func
Prediction in terms of whether a variant causes the variant bearing protein to lose the original function or gain new function is needed for better understanding of how the variant contributes to disease/cancer. Based on HMMvar, HMMvar-func classifies variants into four types of functional outcome: gain, loss, switch, and conservation of function.
PseKNC-General
PseKNC-General (the general form of pseudo k-tuple nucleotide composition), allows for fast and accurate computation of all the widely used nucleotide structural and physicochemical properties of both DNA and RNA sequences. PseKNC-General can generate several modes of pseudo nucleotide compositions, including conventional k-tuple nucleotide compositions, Moreau–Broto autocorrelation coefficient, Moran autocorrelation coefficient, Geary autocorrelation coefficient, Type I PseKNC and Type II PseKNC. In every mode, >100 physicochemical properties are available for choosing. Moreover, it is flexible enough to allow the users to calculate PseKNC with user-defined properties. The package can be run on Linux, Mac and Windows systems and also provides a graphical user interface.
Vindel
Vindel, a simple yet effective computational pipeline, can be used to check whether a set of indels are redundant with respect to those already in the database of interest such as NCBI’s dbSNP. Of the approximately 5.9 million indels we examined, nearly 0.6 million are redundant, revealing a serious limitation in the current indel annotation. Statistics results prove the consistency of the pipeline on indel redundancy detection for all 22 chromosomes.
TransPS
TransPS is a pipeline for post-processing of pre-assembled transcriptomes using reference based method. It applies an align-layout-consensus structure, consisting of three major stages. First, query sequences are aligned with a reference genome. Second, query sequences are ordered based on the alignment to the reference. Third, non-redundant sequences matched to the same gene of reference genome are scaffolded into one contig. The results show that the post processed transcriptome removed the redundant contigs while having significant higher coverage ratio than the original transcriptome.