• STXXL

  • Referenced in 17 articles [sw06824]
  • components, breadth-first search decompositions, constructing suffix arrays, and computing social network analysis metrics...
  • STAR

  • Referenced in 14 articles [sw02515]
  • maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure...
  • libdivsufsort

  • Referenced in 3 articles [sw38865]
  • software library that implements a lightweight suffix array construction algorithm. This library provides a simple ... efficient C API to construct a suffix array and a Burrows-Wheeler transformed string from...
  • mkESA

  • Referenced in 2 articles [sw35130]
  • mkESA: enhanced suffix array construction tool. Summary: We introduce the tool mkESA, an open source ... program for constructing enhanced suffix arrays (ESAs), striving for low memory consumption, yet high practical ... parallelized version of the Deep-Shallow suffix array construction algorithm, which is known ... files with multiple sequences, and computes suffix arrays and various additional tables, such...
  • Big-BWT

  • Referenced in 3 articles [sw34744]
  • build the BWT and optionally the Suffix Array for highly repetitive files using the approach...
  • Fiona

  • Referenced in 3 articles [sw34360]
  • efficient implementation of the partial suffix array to detect read overlaps with different seed lengths...
  • RAPSearch2

  • Referenced in 3 articles [sw23045]
  • suffix array data structure. Here we present RAPSearch2, a new memory-efficient implementation...
  • IGTools

  • Referenced in 2 articles [sw34225]
  • main goal of IGTools, where suffix arrays are a key point in the data structures...
  • GSNAP

  • Referenced in 1 article [sw17306]
  • than four billion bp, and enhanced suffix arrays (ESAs) with novel data structures for fast ... greedy match-and-extend algorithm using suffix arrays, segment chaining using genomic hash tables, diagonalization...
  • KABOOM

  • Referenced in 1 article [sw35129]
  • KABOOM! A new suffix array based algorithm for clustering expression data. Results: We introduce ... efficient implementation using modified suffix arrays. We demonstrate its efficiency by presenting our new expression...
  • GAP

  • Referenced in 3003 articles [sw00320]
  • GAP is a system for computational discrete algebra...
  • LEDA

  • Referenced in 261 articles [sw00509]
  • In the core computer science areas -- data structures...
  • MapReduce

  • Referenced in 253 articles [sw00546]
  • MapReduce is a new parallel programming model initially...
  • R

  • Referenced in 8904 articles [sw00771]
  • R is a language and environment for statistical...
  • LIBSVM

  • Referenced in 1124 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • ALLPATHS

  • Referenced in 15 articles [sw06112]
  • ALLPATHS-LG is a whole-genome shotgun assembler...
  • Soap

  • Referenced in 38 articles [sw08915]
  • SOAP: short oligonucleotide alignment program. We have developed...
  • Quake

  • Referenced in 5 articles [sw12012]
  • Quake is a package to correct substitution sequencing...
  • SOAP3

  • Referenced in 4 articles [sw12017]
  • SOAP3 is a GPU-based software for aligning...