QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform

Shrestha, Ram Krishna; Lubinsky, Baruch; Bansode, Vijay B; Moinz, Mónica B J; McCormack, Grace P.; Travers, Simon

doi:10.1186/1471-2105-15-33

Cited by 25 publications

(22 citation statements)

References 14 publications

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“…The resulting sequences were quality trimmed using QTrim (21). Sequences with a minimum read length of 260bp and a mean quality score of 23 or higher (≥99% confidence) were considered high quality and used for downstream analyses.…”

Section: Methodsmentioning

confidence: 99%

Ability To Develop Broadly Neutralizing HIV-1 Antibodies Is Not Restricted by the Germline Ig Gene Repertoire

Scheepers¹,

Shrestha

Lambson³

et al. 2015

The Journal of Immunology

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The human immunoglobulin repertoire is vast, producing billions of unique antibodies from a limited number of germline immunoglobulin genes. The immunoglobulin heavy chain variable region (IGHV) is central to antigen binding and is comprised of 48 functional genes. Here we analyzed whether HIV-1 infected individuals who develop broadly neutralizing antibodies show a distinctive germline IGHV profile. Using both 454 and Illumina technologies we sequenced the IGHV repertoire of 28 HIV-infected South African women from the Center for the AIDS Programme of Research in South African (CAPRISA) 002 and 004 cohorts, 13 of whom developed broadly neutralizing antibodies. Of the 259 IGHV alleles identified in this study, approximately half were not found in the International Immunogenetics Database (IMGT). This included 85 entirely novel alleles and 38 alleles that matched rearranged sequences in non-IMGT databases. Analysis of the rearranged H chain V region genes of monoclonal antibodies isolated from 7 of the CAPRISA women and previously isolated broadly neutralizing antibodies from other donors provided evidence that at least 8 novel or non-IMGT alleles contributed to functional antibodies. Importantly, we found that despite a wide range in the number of IGHV alleles in each individual, including alleles used by known broadly neutralizing antibodies, there were no significant differences in germline IGHV repertoires between individuals who do and do not develop broadly neutralizing antibodies. This study reports novel IGHV repertoires and highlights the importance of a fully comprehensive immunoglobulin database for germline gene usage prediction. Furthermore, these data suggest a lack of genetic bias in broadly neutralizing antibody development in HIV-1 infection, with implications for HIV vaccine design.

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Section: Methodsmentioning

confidence: 99%

Ability To Develop Broadly Neutralizing HIV-1 Antibodies Is Not Restricted by the Germline Ig Gene Repertoire

Scheepers¹,

Shrestha

Lambson³

et al. 2015

The Journal of Immunology

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“…The Q. suber transcriptome was obtained using tissues at different stages/conditions of development such as: acorns from developmental stage 2 (ERR490202), 3 and 4 (ERR490203) and 5 (ERR490204) [25]; a pool of embryos collected from the acorns of stage 1 to 8 (ERR490207) [25]; cork of bad (SRR1009171) and good (SRR1009172) quality [26]; male (SRR1609152) and female (SRR1609153) flowers [27]; roots of plants with different degrees of watering: medium (SRR1812375), low (SRR1812376) and abundant (SRR1812377) [28]; red and opened buds (SRR5345606) and dormant and swollen buds (SRR5345607) [29]. The libraries where first trimmed to remove SMART adapters, present in the 454 libraries, using AlienTrimmer [30] and then filtered by QTRIM [31] using default quality parameters. Alignment against the Q.…”

Section: Transcriptome Data Analysismentioning

confidence: 99%

Genome-Wide Identification of Epigenetic Regulators inQuercus suber

Silva

Sobral

Magalhães

et al. 2020

Preprint

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Modifications of DNA and histones, including methylation and acetylation, are critical for the epigenetic regulation of gene expression during plant development, particularly during environmental adaptation processes. However, information on the enzymes catalyzing all these modifications in perennial trees, such as Quercus suber, is still not available. In this study, several epigenetic modifier proteins, including eight DNA methyltransferases (DNA Mtases), three DNA demethylases (DDMEs) and ninety-one histone modifiers including thirty-five histone methyltransferases (HMTs), twenty-six histone demethylases (HDMTs), eight histone acetyltransferases (HATs) and twenty-two histone acetylases (HDACs) were identified in Q. suber. Phylogenetic analyses of the DNA and histone modifier proteins were performed using several plant species homologs, enabling the classification of the Q. suber proteins. Additional in silico analysis showed that some Q. suber DNA Mtases, DMEs and histone modifiers have the typical domains found in the plant model Arabidopsis, which might suggest a conserved functional role. A link between the expression levels of each gene in different Q. suber tissues (buds, flowers, acorns, embryos, cork and roots) with the functions already known for their closest homologs in other species was also established. Therefore, the data generated here are important for future studies exploring the role of epigenetic regulators in this economically important species.

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“…Specifically, raw data from sequencing experiments is either assembled (Illumina) using assemblers such as SOAPdenovo (Xie et al, 2014) or Trinity (Grabherr et al, 2011) or filtered based on the raw read quality score (454-pyrosequencing) using programs such as QTrim (Shrestha et al, 2014) or NGS QC Toolkit (Patel and Jain, 2012). In our pipeline, a stringent quality control score of 30 is used to remove low quality reads.…”

Section: Sequence Analysis Pipelinementioning

confidence: 99%

“…Sequence annotation typically uses homology searching using BLAST to either nucleotide or protein sequence databases with programs like BLAST2GO (Conesa et al, 2005) used to perform process level annotation (Stein, 2001). However, the sheer volume of data generated in next-generations sequencing experiments renders such an approach computationally restrictive or very time-consuming.…”

Section: A C C E P T E D Accepted Manuscriptmentioning

confidence: 99%

An efficient transcriptome analysis pipeline to accelerate venom peptide discovery and characterisation

Prashanth

Lewis

2015

Toxicon

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Please cite this article as: Prashanth, J.R., Lewis, R.J., An efficient transcriptome analysis pipeline to accelerate venom peptide discovery and characterisation, Toxicon (2015), doi: 10.1016/ j.toxicon.2015.09.012. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. M A N U S C R I P T A C C E P T E D ACCEPTED MANUSCRIPT AbstractTranscriptome sequencing is now widely adopted as an efficient means to study the chemical diversity of venoms. To improve the efficiency of analysis of these large datasets, we have optimised an analysis pipeline for cone snail venom gland transcriptomes. The pipeline combines ConoSorter with sequence architecture-based elimination and similarity searching using BLAST to improve the accuracy of sequence identification and classification, while reducing requirements for manual intervention. As a proof-of-concept, we used this approach reanalysed three previously published cone snail transcriptomes from diverse dietary groups. Our pipeline method generated similar results to the published studies with significantly less manual intervention. We additionally found undiscovered sequences in the piscovorous C. geographus and vermivorous C. miles and identified sequences in incorrect superfamilies in the molluscivorus C. marmoreus and C. geographus transcriptomes. Our results indicate that this method can improve toxin detection without extending analysis time. While this method was evaluated on cone snail transcriptomes it can be easily optimised to retrieve toxins from other venomous animals.

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QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform

Cited by 25 publications

References 14 publications

Ability To Develop Broadly Neutralizing HIV-1 Antibodies Is Not Restricted by the Germline Ig Gene Repertoire

Ability To Develop Broadly Neutralizing HIV-1 Antibodies Is Not Restricted by the Germline Ig Gene Repertoire

Genome-Wide Identification of Epigenetic Regulators inQuercus suber

An efficient transcriptome analysis pipeline to accelerate venom peptide discovery and characterisation

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