
STXXL
 Referenced in 18 articles
[sw06824]
 components, breadthfirst 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 BurrowsWheeler 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 DeepShallow suffix array construction algorithm, which is known ... files with multiple sequences, and computes suffix arrays and various additional tables, such...

BigBWT
 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 memoryefficient implementation...

IGTools
 Referenced in 3 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 matchandextend 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 3068 articles
[sw00320]
 GAP is a system for computational discrete algebra...

LEDA
 Referenced in 262 articles
[sw00509]
 In the core computer science areas  data structures...

MapReduce
 Referenced in 257 articles
[sw00546]
 MapReduce is a new parallel programming model initially...

R
 Referenced in 9188 articles
[sw00771]
 R is a language and environment for statistical...

LIBSVM
 Referenced in 1155 articles
[sw04879]
 LIBSVM is a library for Support Vector Machines...

ALLPATHS
 Referenced in 15 articles
[sw06112]
 ALLPATHSLG is a wholegenome 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 GPUbased software for aligning...