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Identification of Significant Computational Building Blocks through Comprehensive Investigation of NGS Secondary Analysis Methods
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Replacing suffix trees with enhanced suffix arrays
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Biological Sequence Analysis
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A universal SNP and small-indel variant caller using deep neural networks
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Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
inferredcites →https://doi.org/10.1038/ng.806openalex-snapshot
A framework for variation discovery and genotyping using next-generation DNA sequencing data
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/srep17875openalex-snapshot
Systematic comparison of variant calling pipelines using gold standard personal exome variants
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An Eulerian path approach to DNA fragment assembly
inferredcites →https://doi.org/10.1089/cmb.2009.0238openalex-snapshot
Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies
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Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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A survey of tools for variant analysis of next-generation genome sequencing data
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SOAP: short oligonucleotide alignment program
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Compressed indexing and local alignment of DNA
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ZOOM! Zillions of oligos mapped
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SeqMap: mapping massive amount of oligonucleotides to the genome
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
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SOAP2: an improved ultrafast tool for short read alignment
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot
Fast and accurate long-read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btt273openalex-snapshot
GAGE-B: an evaluation of genome assemblers for bacterial organisms
inferredcites →https://doi.org/10.1093/nar/gkp1137openalex-snapshot
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
inferredcites →https://doi.org/10.1101/201178openalex-snapshot
Scaling accurate genetic variant discovery to tens of thousands of samples
inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
inferredcites →https://doi.org/10.1101/gr.078212.108openalex-snapshot
Mapping short DNA sequencing reads and calling variants using mapping quality scores
inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot
ABySS: A parallel assembler for short read sequence data
inferredcites →https://doi.org/10.1101/gr.097261.109openalex-snapshot
De novo assembly of human genomes with massively parallel short read sequencing
inferredcites →https://doi.org/10.1101/gr.131383.111openalex-snapshot
GAGE: A critical evaluation of genome assemblies and assembly algorithms
inferredcites →https://doi.org/10.1101/gr.7337908openalex-snapshot
ALLPATHS: De novo assembly of whole-genome shotgun microreads
inferredcites →https://doi.org/10.1109/ipdps.2015.96openalex-snapshot
merAligner: A Fully Parallel Sequence Aligner
inferredcites →https://doi.org/10.1109/sfcs.2000.892127openalex-snapshot
Opportunistic data structures with applications
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NIH’s 1-million-volunteer precision medicine study announces first pilot projects
inferredcites →https://doi.org/10.1155/2015/456479openalex-snapshot
A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference
inferredcites →https://doi.org/10.1186/1471-2105-9-128openalex-snapshot
Using quality scores and longer reads improves accuracy of Solexa read mapping
inferredcites →https://doi.org/10.1186/2047-217x-1-18openalex-snapshot
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot
Versatile and open software for comparing large genomes
inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1186/s13742-015-0069-2openalex-snapshot
Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
inferredcites →https://doi.org/10.1371/journal.pbio.1002195openalex-snapshot
Big Data: Astronomical or Genomical?
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SHRiMP: Accurate Mapping of Short Color-space Reads
inferredcites →https://doi.org/10.1371/journal.pcbi.1000491openalex-snapshot
The Origins of Lactase Persistence in Europe
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Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures
inferredcites →https://doi.org/10.1371/journal.pone.0005361openalex-snapshot
Betulin Is a Potent Anti-Tumor Agent that Is Enhanced by Cholesterol
inferredcites →https://doi.org/10.1371/journal.pone.0007767openalex-snapshot
BFAST: An Alignment Tool for Large Scale Genome Resequencing
inferredcites →https://doi.org/10.1371/journal.pone.0023501openalex-snapshot
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
inferredcites →https://doi.org/10.1371/journal.pone.0035495openalex-snapshot
Perceptions and Experiences of Research Participants on Gender-Based Violence Community Based Survey: Implications for Ethical Guidelines
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SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1101/2020.12.22.423964openalex-snapshot
LISA: A Case For Learned Index based Acceleration of Biological Sequence Analysis
inferred← citeshttps://doi.org/10.1109/ipdps.2019.00041openalex-snapshot
Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems
inferred← citeshttps://doi.org/10.1109/ispass51385.2021.00012openalex-snapshot
GenomicsBench: A Benchmark Suite for Genomics
inferred← citeshttps://doi.org/10.1145/3243176.3243197openalex-snapshot
Performance extraction and suitability analysis of multi- and many-core architectures for next generation sequencing secondary analysis
inferred← citeshttps://doi.org/10.70675/2d1f5f53z65ebz4476z88acz990021e9e6d9openalex-snapshot
Scalable and accurate algorithms for computational genomics and dna-based digital storage
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