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Bioinformatics, ISSN 1367-4803, 10/2012, Volume 28, Issue 20, pp. 2678 - 2679
Motivation: The sequence alignment/map (SAM) and the binary alignment/map (BAM) formats have become the standard method of representation of nucleotide... 
RNA-SEQ | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | READS | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Sequence Alignment - standards | Algorithms | Genomics | Humans | High-Throughput Nucleotide Sequencing | Software | Quality Control | Index Medicus
Journal Article
Bioinformatics, ISSN 1367-4803, 09/2018, Volume 34, Issue 18, pp. 3094 - 3100
Abstract Motivation Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high... 
READ ALIGNMENT | RNA | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | LONG SEQUENCES | ALGORITHM | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | LIBRARY | GENERATION | GENOME | BURROWS-WHEELER TRANSFORM | Quantitative Biology - Genomics
Journal Article
Nature Methods, ISSN 1548-7091, 12/2012, Volume 9, Issue 12, pp. 1185 - 1188
Because of ever-increasing throughput requirements of sequencing data, most existing short-read aligners have been designed to focus on speed at the expense of... 
SHORT READ ALIGNMENT | GENOME | ALGORITHM | ULTRAFAST | BIOCHEMICAL RESEARCH METHODS | BURROWS-WHEELER TRANSFORM | Sequence Alignment - methods | Computational Biology - methods | Algorithms | Base Sequence | Humans | Software | Genome | Genomics - methods | Sequence Analysis, DNA - methods | Chromosome mapping | Usage | Methods | Genomes | Index Medicus
Journal Article
PLoS Computational Biology, ISSN 1553-734X, 01/2018, Volume 14, Issue 1, pp. e1005944 - e1005944
The MUMmer system and the genome sequence aligner nucmer included within it are among the most widely used alignment packages in genomics. Since the last major... 
BASIC LOCAL ALIGNMENT | READ ALIGNMENT | SEQUENCE | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | TOOL | Genomics | Methods | Computational biology | Nucleotide sequence | Funding | Data structures | Genomes | Biology | Perl | Gene sequencing | Computer science | Medicine | Biological effects | Alignment | Algorithms | Query processing | Packages | Parallel processing | Software | Bioinformatics | Index Medicus
Journal Article
Journal Article
Genome Biology, ISSN 1474-760X, 04/2013, Volume 14, Issue 4, pp. R36 - R36
TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant... 
HUMAN GENOME | RNA-SEQ | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ULTRAFAST | GENETICS & HEREDITY | PSEUDOGENES | DISCOVERY | READS | Gene Duplication | Sequence Analysis, RNA - methods | Sequence Alignment - methods | Humans | Sensitivity and Specificity | Transcriptome | Gene Fusion | Mutagenesis, Insertional | Software | Index Medicus | Method
Journal Article
Bioinformatics, ISSN 1367-4803, 08/2010, Volume 26, Issue 20, pp. 2534 - 2540
Journal Article
RNA, ISSN 1355-8382, 08/2016, Volume 22, Issue 8, pp. 1120 - 1138
Journal Article
Methods in Molecular Biology, ISSN 1064-3745, 2016, Volume 1374, pp. 241 - 252
Journal Article
Theoretical Computer Science, ISSN 0304-3975, 02/2018, Volume 710, pp. 148 - 157
Recently a compressed index for similar strings, called the (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is... 
Indexes for similar strings | FM-indexes | Suffix arrays | Alignments | Backward search | STORAGE | SHORT READ ALIGNMENT | COMPUTER SCIENCE, THEORY & METHODS | RETRIEVAL | Data Structures and Algorithms | Computer Science
Journal Article