illumiprocessor protocols

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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


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Documentation


Maintainer


  • person_outline Brant C. Faircloth <>

Additional information


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

illumiprocessor in pipeline

2014
PMCID: 4407909
PMID: 25207863
DOI: 10.1111/1755-0998.12328

[…] computer programs used throughout this study are available from https://github.com/faircloth-lab/uce-probe-design, http://github.com/faircloth-lab/phyluce, and https://github.com/faircloth-lab/illumiprocessor under an open-source, bsd-style licence. sequence reads generated as part of this manuscript are available from the ncbi sequence read archive (sra prjna248919). trinity contig […]


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illumiprocessor in publications

 (11)
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 […]

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 […]

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 […]

PMCID: 5604124
PMID: 28934378
DOI: 10.1093/gbe/evx168

[…] 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 […]

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, […]


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