Ibis specifications


Unique identifier OMICS_01151
Name Ibis
Alternative name Improved base identification system
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format INT or CIF with Bustard reads
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Version 1.1.7
Stability Stable
Maintained Yes


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  • person_outline Janet Kelso <>

Ibis article

Ibis citations

PMCID: 3637282

[…] of an illumina genome analyzer iix instrument with paired-end sequencing of 76 + 7 cycles according to the manufacturer’s instructions (illumina). bases and quality scores were generated with the ibis base caller [73]. the reads were then processed based on their indexes and the indexed reads were aligned with the burrows-wheeler aligner (bwa) software [74] to the chimpanzee homologues of 14 […]

PMCID: 3467033

[…] retrieved from the 1000 genomes project (17); the average sequencing coverage for mtdna was 1919× with read lengths of 36 bp (single end)., first, the base quality score was recalibrated with the ibis software using phix 174 sequencing data as the training dataset (18). reads with more than five bases having a quality score <15 were removed from further analysis. the adapter sequences […]

PMCID: 3262807

[…] for single read multiplex experiments with 76 cycles paired-end on the genome analyzer iix platform (v4 sequencing chemistry and v4 cluster generation kit). raw sequences were analyzed with ibis 1.1.2 [20]. paired-end reads from a single cluster were merged if at least 11 bp were overlapping [21]. from this data, reads with more than 5 bases below a quality score of 15 and reads […]

Ibis institution(s)
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
Ibis funding source(s)
Supported by a grant of the Max Plank Society.

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