Benchmarking short sequence mapping tools
暂无分享,去创建一个
Ümit V. Çatalyürek | Doruk Bozdag | Amanda E. Toland | Ayat Hatem | A. Toland | D. Bozdag | A. Hatem | Doruk Bozdag
[1] Steven J. M. Jones,et al. Slider—maximum use of probability information for alignment of short sequence reads and SNP detection , 2008, Bioinform..
[2] D. J. Wheeler,et al. A Block-sorting Lossless Data Compression Algorithm , 1994 .
[3] Michael Q. Zhang,et al. Using quality scores and longer reads improves accuracy of Solexa read mapping , 2008, BMC Bioinformatics.
[4] Giovanni Manzini,et al. Opportunistic data structures with applications , 2000, Proceedings 41st Annual Symposium on Foundations of Computer Science.
[5] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[6] Serban Nacu,et al. Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..
[7] P. Bork,et al. A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.
[8] Michael Brudno,et al. SHRiMP: Accurate Mapping of Short Color-space Reads , 2009, PLoS Comput. Biol..
[9] Knut Reinert,et al. RazerS 3: Faster, fully sensitive read mapping , 2012, Bioinform..
[10] Alok N. Choudhary,et al. FANGS: high speed sequence mapping for next generation sequencers , 2010, SAC '10.
[11] Brian D. Ondov,et al. Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications , 2008, Bioinform..
[12] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[13] Juliane C. Dohm,et al. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing , 2008, Nucleic acids research.
[14] Bin Ma,et al. ZOOM! Zillions of oligos mapped , 2008, Bioinform..
[15] Leping Li,et al. ART: a next-generation sequencing read simulator , 2012, Bioinform..
[16] Huanming Yang,et al. SNP detection for massively parallel whole-genome resequencing. , 2009, Genome research.
[17] Steven J. M. Jones,et al. High quality SNP calling using Illumina data at shallow coverage , 2010, Bioinform..
[18] Nuno A. Fonseca,et al. Tools for mapping high-throughput sequencing data , 2012, Bioinform..
[19] Paul Flicek,et al. Sense from sequence reads: methods for alignment and assembly , 2009, Nature Methods.
[20] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[21] Jan Schröder,et al. Genome analysis SHREC : a short-read error correction method , 2009 .
[22] Véronique Martin,et al. Mapping Reads on a Genomic Sequence: An Algorithmic Overview and a Practical Comparative Analysis , 2012, J. Comput. Biol..
[23] Knut Reinert,et al. A novel and well-defined benchmarking method for second generation read mapping , 2011, BMC Bioinformatics.
[24] K. Reinert,et al. RazerS--fast read mapping with sensitivity control. , 2009, Genome research.
[25] Siu-Ming Yiu,et al. SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..
[26] J. Kitzman,et al. Personalized Copy-Number and Segmental Duplication Maps using Next-Generation Sequencing , 2009, Nature Genetics.
[27] Ümit V. Çatalyürek,et al. Benchmarking Short Sequence Mapping Tools , 2011, BIBM.
[28] Manuel Holtgrewe,et al. Mason – A Read Simulator for Second Generation Sequencing Data , 2010 .
[29] Siu-Ming Yiu,et al. SOAP3: ultra-fast GPU-based parallel alignment tool for short reads , 2012, Bioinform..
[30] Giorgio Valle,et al. PASS: a program to align short sequences , 2009, Bioinform..
[31] P. Green,et al. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.
[32] T. Thomas,et al. GemSIM: general, error-model based simulator of next-generation sequencing data , 2012, BMC Genomics.
[33] Marcel H. Schulz,et al. A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome , 2008, Science.
[34] S. Nelson,et al. BFAST: An Alignment Tool for Large Scale Genome Resequencing , 2009, PloS one.
[35] M. Long,et al. Intron-exon structures of eukaryotic model organisms. , 1999, Nucleic acids research.
[36] Jens Stoye,et al. Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming , 2011, Bioinform..
[37] Faraz Hach,et al. mrsFAST: a cache-oblivious algorithm for short-read mapping , 2010, Nature Methods.
[38] P Green,et al. Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.
[39] Heng Li,et al. A survey of sequence alignment algorithms for next-generation sequencing , 2010, Briefings Bioinform..
[40]
R. Durbin,et al.
Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P ,
2022
.
[41]
Matthew Ruffalo,et al.
Comparative analysis of algorithms for next-generation sequencing read alignment
,
2011,
Bioinform..
[42]
Robert D Schnabel,et al.
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
,
2008,
Nature Methods.
[43]
S. Nelson,et al.
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
,
2008,
Nature.
[44]
Rui Jiang,et al.
Evaluation of next-generation sequencing software in mapping and assembly
,
2011,
Journal of Human Genetics.