TagDust protocols

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TagDust specifications

Information


Unique identifier OMICS_01095
Name TagDust
Alternative name TagDust2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.33
Stability Stable
Maintained Yes

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Publications for TagDust

TagDust in pipelines

 (18)
2018
PMCID: 5930951
PMID: 29716548
DOI: 10.1186/s12864-018-4692-z

[…] was sequenced on an illumina miseq (4 million reads generated per library). the sequencing data was analyzed using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), filtered using tagdust2 [], mapped using bwa [], clustered using paraclu [], and visualized using bedtools [] and the ucsc genome browser []., rsox-4 was lr cloned upstream of a lacz reporter gene directed […]

2017
PMCID: 5338858
PMID: 28212376
DOI: 10.1371/journal.pgen.1006629

[…] was done in 5 replicates., the reads in fastq format generated by illumina sequencing were filtered using fastxclipper from the fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and tagdust [] for adapter removal. trimming of reads was performed using sickle (https://github.com/najoshi/sickle). to assure high sequence quality, we used a cutoff phred score of 20. after trimming, […]

2016
PMCID: 4821887
PMID: 27029645
DOI: 10.1038/ncomms11173

[…] kit at the unc high throughput sequencing facility. pools of 24 multiplexed samples were sequenced per lane on an illumina hiseq 2500 using 50-bp paired-end reads., rna-seq reads were filtered using tagdust and aligned to the reference mouse genome (mm9) with tophat using default parameters. reads aligning to ribosomal rna genes were removed. transcript abundance was estimated by computing reads […]

2016
PMCID: 4832459
PMID: 27079381
DOI: 10.1186/s40478-016-0306-7

[…] and sequenced on a hiseq 2000 (illumina). sequenced reads were demultiplexed, trimmed using the fastx toolkit (fastx toolkit, http://hannonlab.cshl.edu/fastx_toolkit/), filtered for artifacts using tagdust (version 1.12) [] and mapped to the human genome (build grch37/hg19) using the burrows-wheeler aligner (bwa version 0.5.9) [] allowing up to two mismatches. the resulting bam files […]

2016
PMCID: 4883752
PMID: 27231886
DOI: 10.1371/journal.pone.0156439

[…] kit at the unc high throughput sequencing facility. pools of 24 multiplexed samples were sequenced per lane in a hiseq 2500 sequencer using 50 bp paired-end reads., rna-seq reads were filtered using tagdust and aligned to the reference mouse genome (mm9) with tophat using default parameters. reads aligning to rrna genes were removed. transcript abundance was estimated by computing rpkm using […]


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TagDust in publications

 (45)
PMCID: 5904329
PMID: 29674926
DOI: 10.3897/phytokeys.95.21126

[…] two bases of anchor sequences in the 1st primers. the authors used option ‘quality_ filter’ of fastx-toolkit to select reads in which 40% or more sequences had quality scores q30 or more. then the tagdust programme () was used to remove the reads derived from extremely short library entries and to trim read 1 and read 2 sequences. then, loci were assembled from the quality-filtered reads data […]

PMCID: 5677018
PMID: 29116076
DOI: 10.1038/s41467-017-01467-7

[…] hiseq 2500 platform with a read length of 50 bases. sequences with ambiguous base calling were discarded, samples reads split by barcodes and artefactual linker/adapter sequences removed using tagdust (v2.2). reads were of 26–42 bases in length. cage tags were mapped to the reference genome hg19/grch37 using delve (v1.0) and burrows-wheeler aligner (bwa v0.5.6). two mismatches were allowed […]

PMCID: 5625555
PMID: 28972578
DOI: 10.1038/sdata.2017.147

[…] to errors caused by mismatches during the hybridisation to the rnas, that are well tolerated by the reverse-transcriptase., the cage and cagescan reads were then filtered independently with the tagdust program version 1.13 (ref. ), using the sequences of empty constructs and primers as artefact library. they were then compared to reference sequences of ribosomal genes (genbank: u13369.1) […]

PMCID: 5623005
PMID: 29018358
DOI: 10.3389/fphys.2017.00735

[…] using the min elute gel recovery kit (qiagen, valencia, ca, usa) and sequenced using the proton i chip of ion proton™ system (life technology, thermo scientific, wilmington, de, usa). using the tagdust, lucy, and seqclean software programs with default parameters, short or low-quality sequences and adaptor sequences were removed (li and chou, ; chen et al., ; lassmann et al., ). male […]

PMCID: 5574553
PMID: 28850571
DOI: 10.1371/journal.pbio.2002054

[…] sequences were generated at unc-ch htsf. reads were filtered requiring a quality score of 20 or greater in at least 90 percent of nucleotides, and adapter contaminated reads were removed with tagdust []. additionally, no more than 5 reads with identical sequence were retained. nonfiltered reads were aligned with the gsnap software [] to sex-specific hg19 genomes using k-mer size of 15 […]


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TagDust institution(s)
RIKEN Center for Life Science Technologies (CLST), RIKEN Yokohama Institute, Yokohama, Japan; Telethon Kids Institute, The University of Western Australia, Subiaco, WA, Australia
TagDust funding source(s)
Supported by a Research Grant from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) to the RIKEN Center for Life Science Technologies.

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