CONSULT: accurate contamination removal using locality-sensitive hashing

A fundamental question appears in many bioinformatics applications: Does a sequencing read belong to a large dataset of genomes from some broad taxonomic group, even when the closest match in the set is evolutionarily divergent from the query? For example, low-coverage genome sequencing (skimming) projects either assemble the organelle genome or compute genomic distances directly from unassembled reads. Using unassembled reads needs contamination detection because samples often include reads from unintended groups of species. Similarly, assembling the organelle genome needs distinguishing organelle and nuclear reads. While k-mer-based methods have shown promise in read-matching, prior studies have shown that existing methods are insufficiently sensitive for contamination detection. Here, we introduce a new read-matching tool called CONSULT that tests whether k-mers from a query fall within a user-specified distance of the reference dataset using locality-sensitive hashing. Taking advant..., , , # Access to the data used for CONSULT benchmarking

Date belonging to the following paper:

* Rachtman, E., Bafna, V., & Mirarab, S. (2021). CONSULT: accurate contamination removal using locality-sensitive hashing. NAR Genomics and
Bioinformatics. [doi:10.1093/nargab/lqab071](https://doi.org/10.1093/nargab/lqab071)

## Description of the data and file structure

## Drosophila data

Genome and genome skims used for real Drosophila data analysis are provided.

### Before clean-up

#### `Dros_fastq_af_bbmerge.tar`

This file contains deduplicated reads for Drosophila species before clean-up

It contains the following Drosophila species in fq format:

* `sub_Drosophila_ananassae_2.fq.gz`: Drosophila ananassae
* `sub_Drosophila_biarmipes_2.fq.gz`: Drosophila biarmipes
* `sub_Drosophila_bipectinata_2.fq.gz`: Drosophila bipectinata
* `sub_Drosophila_erecta_2.fq.gz`: Drosophila erecta
* `sub_Drosophila_eugracilis_2.fq.gz`: Drosophila eugracilis
* `sub_Drosophila_mauritiana...