Introduction

Smoothq is a sensitive overlap detection program that detects overlaps for long but error-prone DNA reads generated by the third generation sequencing technology such as PacBio SMRT and Oxford Nanopore.

The innovation of Smoothq is to convert q-gram to smooth q-gram via CGK-embedding and resampling, which can capture q-gram paris with small edit distance. Using smooth q-gram instead of q-gram as seeds, Smoothq is very sensitive to detect overlaps between DNA reads even when their overlap length is small.

Getting Started

Compile

git clone git@github.com:FIGOGO/smoothq.git
cd smoothq
cmake .
make

Usage

General usage:

./smoothq input.fasta [options] > overlap.txt

A small dataset ecoli1000.fasta is provided for testing purposes:

./smoothq ecoli1000.fasta -t 4 -q 16 > overlap.txt

Options

The size of the q-gram, cgk-embedding and smooth q-gram can be tune by the following:

• -q, default = 14: q-gram size
• -e, default = 35: embedding size
• -m, default = 16: smooth q-gram size

Parameters controlling the number of signatures (sensitivity) can be tuned by the following:

• -f, default = 5e-4: filtering threshold
• -c, default = 5: minimum number of signature match
• -r, default = 0.2: sampling rate

Number of threads used in the algorithm can be tuned by the following:

• -t, default = 16: number of threads

Output format:

• -o, default = 'm4': accepting both 'm4' and 'paf'

Optional input file:

• -i, default = None: overlap detection between two datasets

Output format

Our output is similar to BLASR’s M4 format.

1. Index of sequence 1 (Index is 1-based)
2. Index of sequence 2
3. Sequence tags in original fasta file separated by '_'
4. Signature density of the overlap
5. Direction of sequence 1 (0 = forward, 1 = reversed)
6. Overlap start position on sequence 1
7. Overlap end position on sequence 1
8. Length of sequence 1
9. Direction of sequence 2 (0 = forward, 1 = reversed)
10. Overlap start position on sequence 2
11. Overlap end position on sequence 2
12. Length of sequence 2

We can also generate output in PAF format if given option '-o paf'.

Acknowledgement

We use the xxHash package in smooth q-gram hashing.