Welcome to kmindex documentation¶
kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks.
Given a databank \(D = \{S_1, ..., S_n\}\), with each \(S_i\) being any genomic dataset (genome or raw reads), kmindex allows to compute the percentage of shared k-mers between a query \(Q\) and each \(S \in D\). It supports multiple datasets and allows searching for each sub-index \(D_i \in G = \{D_1,...,D_m\}\). Queries benefit from the findere algorithm. In a few words, findere allows to reduce the false positive rate at query time by querying \((s+z)\)-mers instead of \(s\)-mers, which are the indexed words, usually called \(k\)-mers.
User guide¶
Server¶
Contact
Teo Lemane: teo[dot]lemane[at]genoscope[dot]cns[dot]fr