Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing

Summary Harmonizing quality control (QC) of large-scale second and third-generation sequencing datasets is key for enabling downstream computational and biological analyses. We present Alfred, an efficient and versatile command-line application that computes multi-sample QC metrics in a read-group aware manner, across a wide variety of sequencing assays and technologies. In addition to standard QC metrics such as GC bias, base composition, insert size and sequencing coverage distributions it supports haplotype-aware and allele-specific feature counting and feature annotation. The versatility of Alfred allows for easy pipeline integration in high-throughput settings, including DNA sequencing facilities and large-scale research initiatives, enabling continuous monitoring of sequence data quality and characteristics across samples. Alfred supports haplo-tagging of BAM/CRAM files to conduct haplotype-resolved analyses in conjunction with a variety of next-generation sequencing based assays. Alfred’s companion web application enables interactive exploration of results and comparison to public datasets. Availability and implementation Alfred is open-source and freely available at https://tobiasrausch.com/alfred/. Supplementary information Supplementary data are available at Bioinformatics online.

DeepSNVMiner: a sequence analysis tool to detect emergent, rare mutations in subsets of cell populations

Background.Massively parallel sequencing technology is being used to sequence highly diverse populations of DNA such as that derived from heterogeneous cell mixtures containing both wild-type and disease-related states. At the core of such molecule tagging techniques is the tagging and identification of sequence reads derived from individual input DNA molecules, which must be first computationally disambiguated to generate read groups sharing common sequence tags, with each read group representing a single input DNA molecule. This disambiguation typically generates huge numbers of reads groups, each of which requires additional variant detection analysis steps to be run specific to each read group, thus representing a significant computational challenge. While sequencing technologies for producing these data are approaching maturity, the lack of available computational tools for analysing such heterogeneous sequence data represents an obstacle to the widespread adoption of this technology.Results.Using synthetic data we successfully detect unique variants at dilution levels of 1 in a 1,000,000 molecules, and find DeeepSNVMiner obtains significantly lower false positive and false negative rates compared to popular variant callers GATK, SAMTools, FreeBayes and LoFreq, particularly as the variant concentration levels decrease. In a dilution series with genomic DNA from two cells lines, we find DeepSNVMiner identifies a known somatic variant when present at concentrations of only 1 in 1,000 molecules in the input material, the lowest concentration amongst all variant callers tested.Conclusions.Here we present DeepSNVMiner; a tool to disambiguate tagged sequence groups and robustly identify sequence variants specific to subsets of starting DNA molecules that may indicate the presence of a disease. DeepSNVMiner is an automated workflow of custom sequence analysis utilities and open source tools able to differentiate somatic DNA variants from artefactual sequence variants that likely arose during DNA amplification. The workflow remains flexible such that it may be customised to variants of the data production protocol used, and supports reproducible analysis through detailed logging and reporting of results. DeepSNVMiner is available for academic non-commercial research purposes athttps://github.com/mattmattmattmatt/DeepSNVMiner.

Clostridium difficile Recurrence Is a Strong Predictor of 30-Day Rehospitalization Among Patients in Intensive Care

ObjectiveWhile incidence, mortality, morbidity, and recurrence rates of C. difficile infection (CDI) among the critically ill have been investigated, the impact of its recurrence on 30-day rehospitalization (ReAd), an important policy focus, has not been examined.DesignSecondary analysis of a multicenter retrospective cohort studyPatientsAdult critically ill patients who survived their index hospitalization complicated by CDIMethodsCDI was defined by diarrhea or pseudomembranous colitis and a positive assay for C. difficile toxins A and/or B. CDI recurrence (rCDI) was defined as diarrhea, positive C. difficile toxin and need for retreatment after cessation of therapy. Descriptive statistics and a logistic regression examined ReAd rates and characteristics, and factors that impact it.ResultsAmong 287 hospital survivors, 76 (26.5%) required ReAd (ReAd+). At baseline, the ReAd+ group did not differ significantly from the ReAd– group based on demographics, comorbidities, APACHE II scores, or ICU type. ReAd+ patients were more likely to have hypotension at CDI onset (48.7% vs 34.1%, P=.025) and to require vasopressors (40.0% vs 27.1%, P=.038); they were less likely to require mechanical ventilation (56.0% vs 77.3%, P<.001). A far greater proportion of ReAd+ than ReAd– had developed a recurrence either during the index hospitalization or within 30 days after discharge (32.89% vs 2.84%, P<.001). In a logistic regression, rCDI was a strong predictor of ReAd+ (adjusted odd ratio, 15.33, 95% confidence interval, 5.68–41.40).ConclusionsGreater than 25% of all survivors of critical illness complicated by CDI require readmission within 30 days of discharge. CDI recurrence is a strong predictor of such rehospitalizations.Infect Control Hosp Epidemiol 2014;00(0): 1–7

Digging for Apples: Reappraising the Influence of Situationist Theory on Theatre Practice in the English Counterculture

This article is a development of a paper submitted to last year's ASTR conference at City University of New York as part of a panel discussion on the legacy of the 1960s. That paper was prepared to the conference brief that submissions should involve some reflexive investigation of research methods and scholarly practices. Reviewing existing material written on the causal links between Situationist theory and theatre practice in the 1960s counterculture in England, I began to question the “fit” between these two areas. A critical narrative concerning the development of a post-Brechtian theatrical style in the work of a generation of English political dramatists — such as Howard Brenton, Trevor Griffiths, and David Edgar — during the late 1960s and early 1970s has come to read Situationism as a dominant shaping force. On closer examination, however, this relationship is neither as clear nor as convincing as this now commonplace critical model would suggest. Additionally, neglected and underreported instances and examples — some of which are explored in this article — seem to tell contrasting, or more complex, stories about the forms and practices of English theatre in the counterculture. Investigation of some of these issues has led me to consider why it is that particular historical orthodoxies develop to account for movements and moments in cultural and performance history. What happens to make a small and, at the time, not widely published or read group of theorists such as the Situationists take on a retrospectively key position in scholarly accounts of cultural history? Thus, this article investigates the transmission of Situationist ideas in English theatre practice to conclude that there may be a broader, more idiosyncratic, history to read against dominant accounts of influence and causation.

Comparison of Reading Programs for Children with Low Levels of Reading Readiness

The present study compared the relative effectiveness of a phonetic approach (Distar) and use of a special alphabet (Johnny Right-to-Read) to reading instruction for children with low levels of reading readiness. Subjects were 12 male and 12 female second graders. While both groups made significant gains in word and paragraph meaning, children in the Distar group made significantly greater gains in reading comprehension than those in the Johnny Right-to-Read group. In addition to the Distar program's emphasis on the development of auditory and visual comprehension skills, the present results might be related to the highly structured presentation and comprehensiveness of this program.