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Academic Journal

GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data.

  • Authors : Ahmed N; Delft University of Technology, Delft, Netherlands and University of Engineering and Technology, Lahore, Pakistan. .; Lévy J

Subjects: Gene Library* ; High-Throughput Nucleotide Sequencing* ; Sequence Alignment*

  • Source: BMC bioinformatics [BMC Bioinformatics] 2019 Oct 25; Vol. 20 (1), pp. 520. Date of Electronic Publication: 2019 Oct 25.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Academic Journal

A performant bridge between fixed-size and variable-size seeding.

  • Authors : Kutzner A; Department of Information Systems, College of Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.; Kim PS

Subjects: High-Throughput Nucleotide Sequencing/High-Throughput Nucleotide Sequencing/High-Throughput Nucleotide Sequencing/*methods ; Sequence Alignment/Sequence Alignment/Sequence Alignment/*methods; Algorithms

  • Source: BMC bioinformatics [BMC Bioinformatics] 2020 Jul 23; Vol. 21 (1), pp. 328. Date of Electronic Publication: 2020 Jul 23.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Academic Journal

A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction.

  • Authors : Moreland BS; Department of Physics, The Ohio State University, Columbus, OH, USA.; Present address: Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH,, USA.

Subjects: Models, Biological* ; Sequence Alignment*; Computational Biology/Computational Biology/Computational Biology/*methods

  • Source: BMC bioinformatics [BMC Bioinformatics] 2019 Aug 19; Vol. 20 (1), pp. 431. Date of Electronic Publication: 2019 Aug 19.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Academic Journal

GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller.

  • Authors : Ren S; Delft University of Technology, Mekelweg 4, Delft, 2628 CD, The Netherlands.; Ahmed N

Subjects: Algorithms* ; Computer Graphics* ; Genetic Variation*

  • Source: BMC genomics [BMC Genomics] 2019 Apr 04; Vol. 20 (Suppl 2), pp. 184. Date of Electronic Publication: 2019 Apr 04.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

pblat: a multithread blat algorithm speeding up aligning sequences to genomes.

  • Authors : Wang M; Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, People's Republic of China.; Kong L

Subjects: Genome, Human* ; Software*; Computational Biology/Computational Biology/Computational Biology/*methods

  • Source: BMC bioinformatics [BMC Bioinformatics] 2019 Jan 15; Vol. 20 (1), pp. 28. Date of Electronic Publication: 2019 Jan 15.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Academic Journal

Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA.

  • Authors : Tang K; Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA.; Ren J

Subjects: Genome, Plant* ; Geography*; DNA, Plant/DNA, Plant/DNA, Plant/*genetics

  • Source: BMC genomics [BMC Genomics] 2018 Dec 10; Vol. 19 (1), pp. 896. Date of Electronic Publication: 2018 Dec 10.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Re-alignment of the unmapped reads with base quality score.

Subjects: Genome, Human* ; High-Throughput Nucleotide Sequencing* ; Software*

  • Source: BMC bioinformatics [BMC Bioinformatics] 2015; Vol. 16 Suppl 5, pp. S8. Date of Electronic Publication: 2015 Mar 18.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Print-Electronic Cited Medium:

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Academic Journal

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC).

Subjects: High-Throughput Nucleotide Sequencing* ; Software*; Computational Biology/Computational Biology/Computational Biology/*methods

  • Source: BMC bioinformatics [BMC Bioinformatics] 2015; Vol. 16 Suppl 7, pp. S10. Date of Electronic Publication: 2015 Apr 23.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Print-Electronic Cited Medium:

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Academic Journal

LW-FQZip 2: a parallelized reference-based compression of FASTQ files.

  • Authors : Huang ZA; College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, 518060, China.; Wen Z

Subjects: Data Compression/Data Compression/Data Compression/*methods ; High-Throughput Nucleotide Sequencing/High-Throughput Nucleotide Sequencing/High-Throughput Nucleotide Sequencing/*methods ; Sequence Alignment/Sequence Alignment/Sequence Alignment/*methods

  • Source: BMC bioinformatics [BMC Bioinformatics] 2017 Mar 20; Vol. 18 (1), pp. 179. Date of Electronic Publication: 2017 Mar 20.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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Academic Journal

Meta-aligner: long-read alignment based on genome statistics.

  • Authors : Nashta-Ali D; Department of Electrical Engineering, Sharif University of Technology, Tehran, Azadi, Iran.; Aliyari A

Subjects: Algorithms* ; Genome, Human*; Sequence Alignment/Sequence Alignment/Sequence Alignment/*methods

  • Source: BMC bioinformatics [BMC Bioinformatics] 2017 Feb 23; Vol. 18 (1), pp. 126. Date of Electronic Publication: 2017 Feb 23.Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium:

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