SeqClean protocols

SeqClean specifications

Information


Unique identifier OMICS_18156
Name SeqClean
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A DNA sequence file.
Input format FASTA
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Requirements blastall, megablast
Maintained Yes

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Maintainers


  • person_outline Geo Pertea <>
  • person_outline PeiIng Hwang <>
  • person_outline Yi-An Chen <>
  • person_outline Chang-Chun Lin <>
  • person_outline Chin-Di Wang <>

Publication for SeqClean

SeqClean IN pipelines

 (4)
2017
PMCID: 5716196
PMID: 29036322
DOI: 10.1093/nar/gkx853

[…] at https://github.com/orgs/schnablelab) which assigned each read to a sample and removed the associated barcode. each debarcoded read was further trimmed to remove proton adaptor sequences using seqclean (sourceforge.net/projects/seqclean) and to remove potentially chimeric reads harboring internal restriction sites of nspi or bfuci. only reads with the correct barcodes and re sites […]

2017
PMCID: 5716196
PMID: 29036322
DOI: 10.1093/nar/gkx853

[…] which assigned each read to a sample and removed the associated barcode. each debarcoded read was further trimmed to remove proton adaptor sequences using seqclean (sourceforge.net/projects/seqclean) and to remove potentially chimeric reads harboring internal restriction sites of nspi or bfuci. only reads with the correct barcodes and re sites were retained for further processing. […]

2013
PMCID: 3667073
PMID: 23734264
DOI: 10.1371/journal.pone.0065902

[…] gs-flx sequencer. the adaptors, low-complexity sequences, sequences with an excess of errors (more than 4% of n) and very short sequences (less than 100 bp) were trimmed by using the lucy [31] and seqclean (http://compbio.dfci.harvard.edu/tgi/). the duplicated reads were eliminated by using cd-hit-454 software [32]. the pre-processed sequences were then subject to assembling using the program […]

2009
PMCID: 2702317
PMID: 19500365
DOI: 10.1186/1471-2164-10-258

[…] after base calling by phred [37], lucy [38] discarded 2,556 low-quality sequences, short or insert-less sequences, and vector or polya-only sequences. an additional 55 sequences were removed by seqclean [39], leaving 10,285 high-quality ests (from 5,450 cdna clones) for further processing (success rate ~80%). assembly of these ests by cap3 [40] resulted in the generation of 1,427 contigs, […]

SeqClean institution(s)
Bioinformatics Core Laboratory, Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan; Lab of Mathematics in Biology, Institute of Statistical Sciences, Academia Sinica, Taipei, Taiwan

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