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Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.

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# OCOCO - the first online variant and consensus caller

[![Build Status](https://travis-ci.org/karel-brinda/ococo.svg?branch=master)](https://travis-ci.org/karel-brinda/ococo)
[![Arxiv](https://img.shields.io/badge/arXiv-1712.01146-green.svg?style=flat)](https://arxiv.org/abs/1712.01146)
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](https://anaconda.org/bioconda/ococo)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1066531.svg)](https://doi.org/10.5281/zenodo.1066531)

## Abstract

**Motivation:** Identifying genomic variants is an essential step for connecting genotype and
phenotype. The usual approach consists of statistical inference of variants
from alignments of sequencing reads. State-of-the-art variant callers can
resolve a wide range of different variant types with high accuracy. However,
they require that all read alignments be available from the beginning of
variant calling and be sorted by coordinates. Sorting is computationally
expensive, both memory- and speed-wise, and the resulting pipelines suffer from
storing and retrieving large alignments files from external memory. Therefore,
there is interest in developing methods for resource-efficient variant calling.

**Results:** We present Ococo, the first program capable of inferring variants in a
real-time, as read alignments are fed in. Ococo inputs unsorted alignments from
a stream and infers single-nucleotide variants, together with a genomic
consensus, using statistics stored in compact several-bit counters. Ococo
provides a fast and memory-efficient alternative to the usual variant calling.
It is particularly advantageous when reads are sequenced or mapped
progressively, or when available computational resources are at a premium.

[![Several-bit Ococo counters](https://raw.githubusercontent.com/karel-brinda/ococo/master/figures/Figure_1.svg)](figures/Figure_1.pdf)

## Citation

> Brinda K, Boeva V, Kucherov G. **Ococo: an online variant and consensus
> caller.** arXiv:1712.01146 [q-bio.GN], 2018. https://arxiv.org/abs/1712.01146

Results from the paper were generated using code in the following repository:
https://github.com/karel-brinda/ococo-paper-analysis.  The entire computation
is also available as a [CodeOcean
capsule](https://codeocean.com/2018/11/14/ococo-colon-an-online-variant-and-consensus-caller).

## Quick example

```bash
git clone --recursive https://github.com/karel-brinda/ococo
cd ococo && make -j
./ococo -i test.bam -f test.fa --vcf-cons -
```

## Installation

### From Bioconda

```
conda install -c bioconda ococo
```

### Building from source

**Prerequisities**

* GCC 4.8+ or equivalent
* ZLib

**Compilation:** ``make``

**Installation:** ``make install``

## How to use

```
SYNOPSIS
       ococo -i <SAM/BAM file> [other options]

DESCRIPTION
       Ococo  is  a  program to call variants and a genomic consensus directly
       from an unsorted SAM/BAM stream.

Input options:
       -i, --input FILE
	      Input SAM/BAM file (- for standard input).

-f, --fasta-ref FILE
	      Initial FASTA reference (otherwise a seq of N's is used).

-s, --stats-in FILE
	      Input statistics.

Output options:
       -F, --fasta-cons FILE Print consensus in FASTA.

-S, --stats-out FILE
	      Export statistics to a file.

-V, --vcf-cons FILE
	      Print inferred variants in VCF (- for standard output).

-P, --pileup FILE
	      Print SAMtools pileup (- for standard output).

--verbose
	      Use the verbose mode (report every update of a counter).

Parameters for consensus calling:
       -x, --counters STR
	      Counter configuration [ococo32].

configuration   bits/counter   bits/position
	      ococo16	      3 	     16
	      ococo32	      7 	     32
	      ococo64	      15	     64

-m, --mode STR
	      Mode [batch].

mode	  description
	      real-time   updates reported immediately
	      batch	  updates reported after end of algn stream

-q, --min-MQ INT
	      Skip alignments with mapping quality smaller than INT [1].

-Q, --min-BQ INT
	      Skip bases with base quality smaller than INT [13].

-w, --ref-weight INT
	      Initial counter value for nucleotides from ref [0].

-c, --min-cov INT
	      Minimum coverage required for update [2].

-M, --maj-thres FLOAT
	      Majority threshold [0.51].

```

## Issues

Please use [Github issues](https://github.com/karel-brinda/ococo/issues).

## Changelog

See [Releases](https://github.com/karel-brinda/ococo/releases).

## Licence

[MIT](https://github.com/karel-brinda/ococo/blob/master/LICENSE)

## Author

[Karel Brinda](http://brinda.cz) \<kbrinda@hsph.harvard.edu\>

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