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Academic Journal

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly.

  • Authors : Sim SB; USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, 64 Nowelo Street, Hilo, HI, 96720, USA. .; Corpuz RL

Subjects: High-Throughput Nucleotide Sequencing* ; Software*; Gene Library

  • Source: BMC genomics [BMC Genomics] 2022 Feb 22; Vol. 23 (1), pp. 157. Date of Electronic Publication: 2022 Feb 22.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

CAMPAREE: a robust and configurable RNA expression simulator.

  • Authors : Lahens NF; The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.; Brooks TG

Subjects: High-Throughput Nucleotide Sequencing* ; Software*; Algorithms

  • Source: BMC genomics [BMC Genomics] 2021 Sep 25; Vol. 22 (1), pp. 692. Date of Electronic Publication: 2021 Sep 25.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data.

  • Authors : Shang GD; National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China.; University of Chinese Academy of Sciences (UCAS), Shanghai, 200032, P. R. China.

Subjects: Software* ; Transcription Factors*/Transcription Factors*/Transcription Factors*/genetics; Chromatin Immunoprecipitation Sequencing

  • Source: BMC genomics [BMC Genomics] 2022 Apr 07; Vol. 23 (Suppl 1), pp. 272. Date of Electronic Publication: 2022 Apr 07.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Genion, an accurate tool to detect gene fusion from long transcriptomics reads.

  • Authors : Karaoglanoglu F; School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.; Vancouver Prostate Centre, Vancouver, BC, Canada.

Subjects: Software* ; Transcriptome*; Gene Fusion

  • Source: BMC genomics [BMC Genomics] 2022 Feb 14; Vol. 23 (1), pp. 129. Date of Electronic Publication: 2022 Feb 14.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

NGS-Integrator: An efficient tool for combining multiple NGS data tracks using minimum Bayes' factors.

  • Authors : Wen B; Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.; Jung HJ

Subjects: High-Throughput Nucleotide Sequencing* ; Software*; Animals

  • Source: BMC genomics [BMC Genomics] 2020 Nov 19; Vol. 21 (1), pp. 806. Date of Electronic Publication: 2020 Nov 19.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Optimizing performance of GATK workflows using Apache Arrow In-Memory data framework.

  • Authors : Ahmad T; Accelerated Big Data Systems Group, Quantum & Computer Engineering Department, Delft University of Technology, Delft, The Netherlands. .; Ahmed N

Subjects: High-Throughput Nucleotide Sequencing* ; Software*; Genomics

  • Source: BMC genomics [BMC Genomics] 2020 Nov 18; Vol. 21 (Suppl 10), pp. 683. Date of Electronic Publication: 2020 Nov 18.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing.

  • Authors : Liu Q; Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.; Hu Y

Subjects: Software* ; Transcriptome*; Algorithms

  • Source: BMC genomics [BMC Genomics] 2020 Dec 29; Vol. 21 (Suppl 11), pp. 793. Date of Electronic Publication: 2020 Dec 29.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data.

  • Authors : Leung CM; Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong. .; L3 Bioinformatics Limited, Rm 2114, Hong Kong Plaza, 188 Connaught Road West, Sai Ying Pun, Hong Kong. .

Subjects: Metagenomics* ; Software*; Algorithms

  • Source: BMC genomics [BMC Genomics] 2020 Dec 21; Vol. 21 (Suppl 6), pp. 500. Date of Electronic Publication: 2020 Dec 21.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data.

  • Authors : Shahryary Y; Technical University of Munich, Institute for Advanced Study (IAS), Lichtenbergstr. 2a, Garching, 85748, Germany.; Technical University of Munich, Department of Plant Sciences, Liesel-Beckmann-Str. 2, Freising, 85354, Germany.

Subjects: DNA Methylation* ; Software* ; Sulfites*

  • Source: BMC genomics [BMC Genomics] 2020 Jul 13; Vol. 21 (1), pp. 479. Date of Electronic Publication: 2020 Jul 13.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis.

  • Authors : Trümbach D; Institute of Developmental Genetics, Helmholtz Zentrum Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.; Pfeiffer S

Subjects: Apoptosis* ; CRISPR-Cas Systems* ; High-Throughput Nucleotide Sequencing*

  • Source: BMC genomics [BMC Genomics] 2017 Nov 25; Vol. 18 (1), pp. 905. Date of Electronic Publication: 2017 Nov 25.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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