Querying large read collections in main memory: a versatile data structure

[1]  Jan Schröder,et al.  BIOINFORMATICS ORIGINAL PAPER , 2022 .

[2]  Carl Kingsford,et al.  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..

[3]  Lucian Ilie,et al.  HiTEC: accurate error correction in high-throughput sequencing data , 2011, Bioinform..

[4]  Heng Li,et al.  A survey of sequence alignment algorithms for next-generation sequencing , 2010, Briefings Bioinform..

[5]  Thomas C. Conway,et al.  Succinct data structures for assembling large genomes , 2010, Bioinform..

[6]  Faraz Hach,et al.  mrsFAST: a cache-oblivious algorithm for short-read mapping , 2010, Nature Methods.

[7]  S. Koren,et al.  Assembly algorithms for next-generation sequencing data. , 2010, Genomics.

[8]  Leena Salmela,et al.  Correction of sequencing errors in a mixed set of reads , 2010, Bioinform..

[9]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[10]  Tom H. Pringle,et al.  Complete Khoisan and Bantu genomes from southern Africa , 2010, Nature.

[11]  J. Tarhio,et al.  Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity , 2009, Nucleic acids research.

[12]  N. Blow Transcriptomics: The digital generation , 2009, Nature.

[13]  Robert Giegerich,et al.  mkESA: enhanced suffix array construction tool , 2009, Bioinform..

[14]  Lee T. Sam,et al.  Transcriptome Sequencing to Detect Gene Fusions in Cancer , 2009, Nature.

[15]  F. Denoeud,et al.  Annotating genomes with massive-scale RNA sequencing , 2008, Genome Biology.

[16]  Rodrigo González,et al.  Compressed text indexes: From theory to practice , 2007, JEAL.

[17]  William F. Smyth,et al.  A taxonomy of suffix array construction algorithms , 2007, CSUR.

[18]  Giovanni Manzini,et al.  Two Space Saving Tricks for Linear Time LCP Array Computation , 2004, SWAT.

[19]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[20]  Rajeev Raman,et al.  Succinct indexable dictionaries with applications to encoding k-ary trees and multisets , 2002, SODA '02.

[21]  Hiroki Arimura,et al.  Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications , 2001, CPM.

[22]  Giovanni Manzini,et al.  Opportunistic data structures with applications , 2000, Proceedings 41st Annual Symposium on Foundations of Computer Science.

[23]  김동규,et al.  [서평]「Algorithms on Strings, Trees, and Sequences」 , 2000 .

[24]  Martin Vingron,et al.  q-gram based database searching using a suffix array (QUASAR) , 1999, RECOMB.

[25]  Z. Galil,et al.  Pattern matching algorithms , 1997 .

[26]  Fei Shi,et al.  Suffix Arrays for Multiple Strings: A Method for On-Line Multiple String Searches , 1996, ASIAN.

[27]  Eugene W. Myers,et al.  Suffix arrays: a new method for on-line string searches , 1993, SODA '90.

[28]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[29]  Peter Weiner,et al.  Linear Pattern Matching Algorithms , 1973, SWAT.

[30]  T. Lecroq,et al.  Querying large read collections in main memory: a versatile data structure , 2011 .

[31]  B. Schmidt,et al.  SHREC: a short-read error correction method , 2009, Bioinform..

[32]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..

[33]  Clifford Stein,et al.  Introduction to Algorithms, 2nd edition. , 2001 .

[34]  Ronald L. Rivest,et al.  Introduction to Algorithms , 1990 .