https://github.com/karel-brinda/ococo

Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
https://github.com/karel-brinda/ococo

bioinformatics consensus ngs online-algorithms variant-calling

Last synced: 8 months ago
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Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.

• Host: GitHub
• URL: https://github.com/karel-brinda/ococo
• Owner: karel-brinda
• License: mit
• Created: 2015-10-30T17:26:34.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2019-01-18T23:40:58.000Z (over 6 years ago)
• Last Synced: 2023-10-20T20:54:28.008Z (almost 2 years ago)
• Topics: bioinformatics, consensus, ngs, online-algorithms, variant-calling
• Language: C++
• Homepage: https://arxiv.org/abs/1712.01146
• Size: 3.49 MB
• Stars: 47
• Watchers: 9
• Forks: 4
• Open Issues: 10
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# 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](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  [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) \