illumiprocessor statistics

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Citations per year

Number of citations per year for the bioinformatics software tool illumiprocessor
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Tool usage distribution map

This map represents all the scientific publications referring to illumiprocessor per scientific context
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Protocols

illumiprocessor specifications

Information


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
Requirements
Java, trimmomatic
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Brant C. Faircloth

Additional information


http://illumiprocessor.readthedocs.io/en/latest/

illumiprocessor citations

 (13)
library_books

Multiple origins of green blood in New Guinea lizards

2018
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 […]

library_books

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

2018
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 […]

library_books

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

2017
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 […]

library_books

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

2017
Genome Biol Evol
PMCID: 5604124
PMID: 28934378
DOI: 10.1093/gbe/evx168

[…] on demultiplexed raw reads from BCL files using bcl2fastq2 ver. 2.17.1.14 (Illumina Inc.) and returned FASTQ-formatted files to us. We trimmed low-quality bases and adapter sequences from reads using illumiprocessor ver. 2 (https://github.com/faircloth-lab/illumiprocessor; last accessed September 1, 2017), which incorporates trimmomatic (). We used the Python package PHYLUCE () for subsequent data […]

library_books

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

2017
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 […]

library_books

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

2017
PeerJ
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 http://phyluce.readthedocs.io/en/latest/quality-control.html and used the parallel wrapper script Illumiprocessor (http://dx.doi.org/10.6079/J9ILL). Clean reads were assembled using the de novo assembler IDBA (), following the pipeline available at: http://phyluce.readthedocs.io/en/latest/assembly […]


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