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illumiprocessor specifications


Unique identifier OMICS_10302
Name illumiprocessor
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 2.0.8
Stability Stable
Java, trimmomatic
Maintained Yes


No version available



  • person_outline Brant C. Faircloth

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illumiprocessor citations


Multiple origins of green blood in New Guinea lizards

Sci Adv
PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] foundation (oklahoma city, ok) for 150-bp paired-end sequencing on an illumina hiseq3000., to process demultiplexed raw reads for phylogenomic analyses, we followed the standard phyluce pipeline (). illumiprocessor, in combination with trimmomatic, was used to filter low-quality reads and remove adapters (, ), yielding an average of 8,504,473 reads (302,468 to 119,426,985) and 1,141,548,626 bp […]


Phylogenomic reclassification of the world’s most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution

Sci Rep
PMCID: 5785998
PMID: 29374214
DOI: 10.1038/s41598-018-19946-2

[…] illumina hiseq. 2500 (brigham young university dna sequencing center)., raw demultiplexed reads were processed with the phyluce pipeline. quality control and adapter removal were conducted with the illumiprocessor wrapper. assemblies were created with velvet and trinity, both at default settings. contigs from both assemblies were combined for probe matching, retrieving assembly-specific uces […]


Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf weevils

PLoS One
PMCID: 5699822
PMID: 29166661
DOI: 10.1371/journal.pone.0188044

[…] are stored in museum collections (snsb-zoological state collection, münchen (zsm), state museum of natural history karlsruhe (smnk), california academy of sciences (cas)), see for details., we used illumiprocessor [], which is a parallel wrapper of trimmomatic [–], to clean and trim reads. we performed this step for each of the two sequencing runs, we then concatenated the two different […]


Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements

Genome Biol Evol
PMCID: 5604124
PMID: 28934378
DOI: 10.1093/gbe/evx168

[…] demultiplexed raw reads from bcl files using bcl2fastq2 ver. (illumina inc.) and returned fastq-formatted files to us. we trimmed low-quality bases and adapter sequences from reads using illumiprocessor ver. 2 (; last accessed september 1, 2017), which incorporates trimmomatic (). we used the python package phyluce () for subsequent […]


Dry habitats were crucibles of domestication in the evolution of agriculture in ants

PMCID: 5394666
PMID: 28404776
DOI: 10.1098/rspb.2017.0095

[…] the phyluce v. 1.4 software package [] and associated programs (see electronic supplementary material, table s2 for all sequencing and assembly statistics). we cleaned and trimmed raw reads using illumiprocessor [] and assembled contigs de novo using trinity v. r2013-02-25 []. after assembly, we used several phyluce scripts to identify and extract uce contigs, remove potential paralogs, […]


Tectonic collision and uplift of Wallacea triggered the global songbird radiation

Nat Commun
PMCID: 5013600
PMID: 27575437
DOI: 10.1038/ncomms12709

[…] hiseq 2500 system at the university of kansas genome sequencing core., we de-multiplexed raw reads using casava ver. 1.8.2 and trimmed low-quality bases and adaptor sequences from reads using illumiprocessor ver. 1 ( which batch processed reads using scythe ( and sickle […]

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