tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.

Read clustering software tools | Whole-genome sequencing data analysis

Sequence clustering can be viewed as a community detection problem on graphs, where nodes represent sequences and edges represent matches between related sequences.Source text:(Zorita et al., 2015) Starcode: sequence clustering based on all-pairs…
G T A T C G C T A
SHARAKU
Desktop

SHARAKU SHape Aligner of non-coding RNA developed by Keio University

Aligns two read mapping profiles of next-generation sequencing outputs for…

Aligns two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping…

G T A T C G C T A
Rainbow
Desktop

Rainbow

Provides an ultra-fast and memory-efficient solution to clustering and…

Provides an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a…

G T A T C G C T A
Starcode
Desktop

Starcode

An exact algorithm to determine which pairs of sequences lie within a given…

An exact algorithm to determine which pairs of sequences lie within a given Levenshtein distance. For error correction or redundancy reduction purposes, matched pairs are then merged into clusters of…

CD-HIT
Desktop
Web

CD-HIT

A widely used program for clustering biological sequences to reduce sequence…

A widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of…

G T A T C G C T A
QCluster
Desktop

QCluster

A family of alignment-free measures, called Dq-type, that incorporate quality…

A family of alignment-free measures, called Dq-type, that incorporate quality value information and k-mers counts for the comparison of reads data. A set of experiments on simulated and real reads…

G T A T C G C T A
ICC
Desktop

ICC Indel and Carryforward Correction

Provides a complete software pipeline for users to analyze pyrosequencing data…

Provides a complete software pipeline for users to analyze pyrosequencing data for both library and amplicon applications. ICC is specifically designed to correct indel and carryforward and…

G T A T C G C T A
GraphClust
Desktop

GraphClust

Compars and clusters RNAs according to sequence and structure. GraphClust…

Compars and clusters RNAs according to sequence and structure. GraphClust scales to datasets of hundreds of thousands of sequences. The quality of the retrieved clusters has been benchmarked against…

G T A T C G C T A
SEED
Desktop

SEED

An efficient algorithm for clustering very large NGS sets. It joins sequences…

An efficient algorithm for clustering very large NGS sets. It joins sequences into clusters that can differ by up to three mismatches and three overhanging residues from their virtual center. It is…

G T A T C G C T A
SlideSort
Desktop

SlideSort

A fast and exact method that can find all similar pairs from a string pool in…

A fast and exact method that can find all similar pairs from a string pool in terms of edit distance. SlideSort can find similar pairs within edit-distance d, from sequences whose length range from…

G T A T C G C T A
Afcluster
Desktop

Afcluster alignment free clustering

Analyses sequence. Afcluster allows to perform assembly with reduced resources…

Analyses sequence. Afcluster allows to perform assembly with reduced resources and a minimal loss of quality. It allows soft expectation maximization (EM) clustering, in which case each sequence is…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.