freeIbis protocols

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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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Maintainer


  • person_outline Gabriel Renaud <>

Publication for freeIbis

freeIbis in pipelines

 (4)
2017
PMCID: 5501502
PMID: 28695206
DOI: 10.1126/sciadv.1700186

[…] hiseq lanes. the captured library a4928 was sequenced on 12% of a miseq lane. sequencing was performed using paired-end runs with double-index configuration ()., base calling was carried out using freeibis () and bustard (illumina) for hiseq and miseq runs, respectively. adapter sequences were removed and overlapping forward and reverse reads were merged using leehom (). sequences […]

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 (), trained on ϕx174 control reads. reads with more than five bases below a base quality score of 10 were excluded. adapter sequences were trimmed and all remaining reads […]

2016
PMCID: 5110243
PMID: 27669147
DOI: 10.7554/eLife.18683.030

[…] in 100-bp paired-end mode on one lane of an illumina hiseq 2500 platform (rapid mode)., base-calling, adaptor trimming and demultiplexing of reads was performed using a custom pipeline based on freeibis (), leehom () and deml (). demultiplexed reads were mapped using tophat v2.0.14, and fpkm (fragments per kilobase of transcript per million mapped reads) values per gene were quantified […]

2016
PMCID: 5312299
PMID: 27463017
DOI: 10.18632/oncotarget.10827

[…] carried out., sequencing was performed on illumina miseq and hiseq instruments with parameters outlined in detail in . base calling was performed by bustard (illumina corp.) for miseq data and by freeibis [] for hiseq data. illumina adapters were removed, putative chimeric sequences were flagged as failing quality control and overlapping paired reads were merged using leehom […]


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freeIbis in publications

 (8)
PMCID: 5727115
PMID: 29234095
DOI: 10.1038/s41598-017-17728-w

[…] previous studies,. libraries were pooled and sequenced in illumina hiseq. 2500 on two rapid lanes with 100 + 7 + 100 + 7 cycles. the kit for the chemistry was v2., base-calling was performed using freeibis, and reads were processed as follows,: read adaptors were trimmed, and reads were filtered for at most 5 bases with a quality score <15, and indexes for no bases with quality scores […]

PMCID: 5336659
PMID: 28259138
DOI: 10.1186/s12862-017-0904-4

[…] for evolutionary anthropology (leipzig, germany). afterwards, illumina paired-end reads (140 bp) were sorted according their indices, adapters were clipped and base calling was conducted with freeibis []. reads with false paired indices were discarded, and overlapping paired-end reads were trimmed and merged to a single sequence []., illumina raw reads were trimmed (10 bp) at both ends […]

PMCID: 5312299
PMID: 27463017
DOI: 10.18632/oncotarget.10827

[…] carried out., sequencing was performed on illumina miseq and hiseq instruments with parameters outlined in detail in . base calling was performed by bustard (illumina corp.) for miseq data and by freeibis [] for hiseq data. illumina adapters were removed, putative chimeric sequences were flagged as failing quality control and overlapping paired reads were merged using leehom […]

PMCID: 4991838
PMID: 27436340
DOI: 10.1093/dnares/dsw029

[…] and custom scripts have to be written to adjust for adna specifics. base calling is frequently performed with illumina’s standard base-caller bustard bayescall (flexible model-based tool) and freeibis (utilizing a multiclass support vector machine algorithm). fastqc is typically used for preliminary quality control of reads. adapterremoval, cutadapt, and seqprep are currently […]

PMCID: 4822957
PMID: 27049965
DOI: 10.1371/journal.pgen.1005972

[…] fragments using empirical sequencing error rates from a phix library (illumina corp.) sequenced at the max planck institute for evolutionary anthropology on an illumina hiseq, basecalled using freeibis []. with the same empirical phix dataset distribution, we generated quality scores for each nucleotide. fragments were mapped back to a random individual from the contaminant panel. shows […]


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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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