freeIbis protocols

freeIbis specifications

Information


Unique identifier OMICS_02217
Name freeIbis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format INT, CIF with Bustard reads
Biological technology Illumina
Operating system Unix/Linux
Programming languages C, Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for freeIbis

freeIbis IN pipelines

 (2)
2016
PMCID: 4860691
PMID: 26979798
DOI: 10.1093/gbe/evw059

[…] following vendor protocols, obtaining 75-bp paired-end reads. hiseq sequencing runs were analyzed starting from raw intensities. base calling and quality score calculation were performed using the freeibis base caller (renaud et al. 2013), trained on ϕx174 control reads. reads with more than five bases below a base quality score of 10 were excluded. adapter sequences were trimmed […]

2015
PMCID: 4505326
PMID: 26183383
DOI: 10.1038/srep12072

[…] described46. the libraries were sequenced as 125 bp paired-end run for r. multicaudata and 96 bp paired-end run for trypanobia sp., both on an illumina hi-seq 2000. base calling was performed with freeibis47, adaptor and primer sequences were removed using leehom48, and reads with low complexity and false paired indices were discarded. raw data of all libraries were trimmed by removing […]

freeIbis institution(s)
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
freeIbis funding source(s)
The Max Planck Society

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