Alternative content
kallisto
Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets)
Software (C++)
https://pachterlab.github.io/kallisto/
Sailfish
Estimation of isoform abundances from reference sequences and RNA-seq data (k-mer based)
Software (C++)
http://www.cs.cmu.edu/~ckingsf/software/sailfish/
Salmon
Quantification of the expression of transcripts using RNA-seq data (uses k-mers)
https://combine-lab.github.io/salmon/
RNA-Skim
RNA-seq quantification at transcript-level (partitions the transcriptome into disjoint transcript clusters; uses sig-mers, a special type of k-mers)
Software (C++)
Variant calling
ChimeRScope
Fusion transcript prediction using gene k-mers profiles of the RNA-seq paired-end reads
Software (Java)
https://github.com/ChimeRScope/ChimeRScope/wiki
FastGT
Genotyping of known SNV/SNP variants directly from raw NGS sequence reads by counting unique k-mers
Software (C)
https://github.com/bioinfo-ut/GenomeTester4/
Phy-Mer
Reference-independent mitochondrial haplogroup classifier from NGS data (k-mer based)
Software (Python)
https://github.com/danielnavarrogomez/phy-mer
LAVA
Genotyping of known SNPs (dbSNP and Affymetrix's Genome-Wide Human SNP Array) from raw NGS reads (k-mer based)
Software (C)
MICADo
Detection of mutations in targeted third-generation NGS data (can distinguish patients’ specific mutations; algorithm uses k-mers and is based on colored de Bruijn graphs)
Software (Python)
General mapper
Minimap
Lightweight and fast read mapper and read overlap detector (uses the concept of “minimazers”, a special type of k-mers)
Software (C)
https://github.com/lh3/minimap
Assembly
De novo genome assembly
MHAP
Produces highly continuous assembly (fully resolved chromosome arms) from third-generation long and noisy reads (10 kbp) using a dimensionality reduction technique MinHash
Software (Java)
Miniasm
Assembler of long noisy reads (SMRT, ONT) using the Overlap-Layout Consensus (OLC) approach without the necessity of an error correction stage (uses minimap)
Software (C)
https://github.com/lh3/miniasm
LINKS
Scaffolding genome assembly with error-containing long sequence (e.g., ONT or PacBio reads, draft genomes)
Software (Perl)
https://github.com/warrenlr/LINKS/
Read clustering
afcluster
Clustering of reads from different genes and different species based on k-mer counts
Software (C++)
https://github.com/luscinius/afcluster
QCluster
Clustering of reads with alignment-free measures (k-mer based) and quality values
Software (C++)
http://www.dei.unipd.it/~ciompin/main/qcluster.html
Reads error correction
Lighter
Correction of sequencing errors in raw, whole genome sequencing reads (k-mer based)
Software (C++)
https://github.com/mourisl/Lighter
QuorUM
Error corrector for Illumina reads using k-mers
Software (C++)
https://github.com/gmarcais/Quorum
Trowel
Software (C++)
https://sourceforge.net/projects/trowel-ec/
Metagenomics
Assembly-free phylogenomics
AAF
Phylogeny reconstruction directly from unassembled raw sequence data from whole genome sequencing projects; provides bootstrap support to assess uncertainty in the tree topology (k-mer based)
Software (Python)
https://github.com/fanhuan/AAF
kSNP v3
Reference-free SNP identification and estimation of phylogenetic trees using SNPs (based on k-mer analysis)
Software (C)
https://sourceforge.net/projects/ksnp/files/
NGS-MC
Phylogeny of species based on NGS reads using alignment-free sequence dissimilarity measures d2* and d2 S under different Markov chain models (using k-words)
R package
http://www-rcf.usc.edu/~fsun/Programs/NGS-MC/NGS-MC.html
Species identification/taxonomic profiling
CLARK
Taxonomic classification of metagenomic reads to known bacterial genomes using k-mer search and LCA assignment
Software (C++)
FOCUS
Reports organisms present in metagenomic samples and profiles their abundances (uses composition-based approach and non-negative least squares for prediction)
Web service Software (Python)
http://edwards.sdsu.edu/FOCUS/
GSM
Estimation of abundances of microbial genomes in metagenomic samples (k-mer based)
Software (Go)
https://github.com/pdtrang/GSM
Mash
Species identification using assembled or unassembled Illumina, PacBio, and ONT data (based on MinHash dimensionality-reduction technique)
Software (C++)
Kraken
Taxonomic assignment in metagenome analysis by exact k-mer search; LCA assignment of short reads based on a comprehensive sequence database
Software (C++)
https://ccb.jhu.edu/software/kraken/
LMAT
Assignment of taxonomic labels to reads by k-mers searches in precomputed database
Software (C++/Python)
https://sourceforge.net/projects/lmat/
stringMLST
k-mer-based tool for MLST directly from the genome sequencing reads
Software (Python)
http://jordan.biology.gatech.edu/page/software/stringMLST
Taxonomer
k-mer-based ultrafast metagenomics tool for assigning taxonomy to sequencing reads from clinical and environmental samples
Web service
Other
d2-tools
Word-based (k-tuple) comparison (pairwise dissimilarity matrix using d2S measure) of metatranscriptomic samples from NGS reads
Software (Python/R)
https://code.google.com/p/d2-tools/
VirHostMatcher
Prediction of hosts from metagenomic viral sequences based on ONF using various distance measures (e.g., d2)
Software (C++)
https://github.com/jessieren/VirHostMatcher
MetaFast
Statistics calculation of metagenome sequences and the distances between them based on assembly using de Bruijn graphs and Bray–Curtis dissimilarity measure
Software (Java)
Comments
AlFree tool for alingment of sequence at http://150.254.122.234:8000/