• BLAT

  • Referenced in 34 articles [sw16891]
  • alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing ... from an index of all nonoverlapping K-mers in the genome. This index fits inside ... alignment between homologous regions. It stitches together these aligned regions (often exons) into larger alignments ... sensitivity are explored for various K-mer sizes, mismatch schemes, and number of required index...
  • Pash

  • Referenced in 1 article [sw34370]
  • Pash 3.0 makes use of gapped k-mer alignment, a non-seed based comparison method...
  • QCluster

  • Referenced in 2 articles [sw34400]
  • error correction. Several alignment-free measures, based on k-mers counts, have been used ... exploit quality value information within the alignment-free framework. In this paper we present ... alignment-free measures, called D q -type, that incorporate quality value information and k-mers ... measures are superior to other classical alignment-free statistics, especially when erroneous reads are considered...
  • IDBA-UD

  • Referenced in 6 articles [sw17029]
  • aligned to contigs and assembled locally to generate some missing k-mers in low-depth...
  • ALFRED

  • Referenced in 1 article [sw22013]
  • Practical Method for Alignment-Free Distance Computation. Alignment-free approaches are gaining persistent interest ... sequence datasets. Besides the widely used k-mer methods, the average common substring (ACS) approach ... well-known alignment-free approaches. Two recent works further generalize this ACS approach by allowing...
  • MotifClick

  • Referenced in 2 articles [sw29728]
  • local gapless alignments between the two 2(k-1)-mers is greater than a cutoff ... motif as a set of similar k-mers from a merged group of maximum cliques...
  • Magnus-Representation

  • Referenced in 1 article [sw34682]
  • representation of genome sequences. We introduce an alignment-free method, the Magnus representation, to analyze ... approach with the idea of k-mers to define an effectively computable mean Magnus vector...
  • SlideSort

  • Referenced in 1 article [sw28786]
  • novo genome assembly, genome-wide alignment and other important analyses. Results: In this study ... algorithm, SlideSort discovers chains of common k-mers to narrow down the search. Compared...
  • Quake

  • Referenced in 4 articles [sw12012]
  • Quake is a package to correct substitution sequencing...
  • Voom

  • Referenced in 17 articles [sw14009]
  • Voom: precision weights unlock linear model analysis tools...
  • SSAKE

  • Referenced in 7 articles [sw16990]
  • SSAKE is a de novo assembler for short...
  • SEQuel

  • Referenced in 2 articles [sw16992]
  • SEQuel is a tool for correcting errors (i.e...
  • Velvet

  • Referenced in 25 articles [sw17026]
  • Velvet: Algorithms for de novo short read assembly...
  • TopHat

  • Referenced in 22 articles [sw17157]
  • TopHat2: accurate alignment of transcriptomes in the presence...
  • RSEM

  • Referenced in 11 articles [sw17160]
  • RSEM: accurate transcript quantification from RNA-Seq data...
  • KMC

  • Referenced in 3 articles [sw20510]
  • KMC — K-mer Counter is a utility designed...
  • Bowtie 2

  • Referenced in 20 articles [sw29190]
  • Bowtie 2 is an ultrafast and memory-efficient...
  • Salmon

  • Referenced in 3 articles [sw31865]
  • Salmon is a wicked-fast program to produce...
  • Yanagi

  • Referenced in 1 article [sw33123]
  • Yanagi: transcript segment library construction for RNA-seq...
  • RapMap

  • Referenced in 1 article [sw33125]
  • RapMap is a testing ground for ideas in...