Galaxy |

ococo (version 0.1.2.6)

SAM/BAM dataset:

Select fasta reference:

Counter configuration: [ococo16]:

Strategy for updates: [majority]:

Save output(s):

Determine which output file(s) to keep

Minimum mapping quality score:

skip alignments with mapping quality smaller than INT [1]

Minimum base quality score:

skip bases with base quality smaller than INT [13]

Initial nucleotides counter:

initial counter value for nucleotides from ref [0]

Minimum coverage required:

minimum coverage required for update [2]

Majority consensus threshold [0.51]:

OCOCO - Online Consensus Caller

OCOCO is a online consensus caller, capable to infer SNVs dynamically as read alignments are fed in. OCOCO inputs unsorted alignments from an unsorted SAM/BAM stream and decides about single-nucleotide updates of the current genomic consensus using statistics stored in compact several-bits counters. Updates are reported in the online fashion using unsorted VCF. OCOCO provides a fast and memory-efficient alternative to the usual variant calling, particularly advantageous when reads are sequenced or mapped progressively, or when available computational resources are at a premium.