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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

Additional information

illumiprocessor citations


Multiple origins of green blood in New Guinea lizards

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

[…] 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 (4 […]


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

[…] an 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 and […]


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

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

[…] 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 sequenci […]


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

[…] on 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 data […]


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

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

[…] ing 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, and ad […]


Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data

PMCID: 5660876
PMID: 29085750
DOI: 10.7717/peerj.3941

[…] g adapter sequences and low quality bases. For this, we followed the analytical pipeline available at and used the parallel wrapper script Illumiprocessor ( Clean reads were assembled using the de novo assembler IDBA (), following the pipeline available at: […]


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