SeqClean protocols

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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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Documentation


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

 (59)
2017
PMCID: 5397604
PMID: 28431015
DOI: 10.1093/dnares/dsw056

[…] e-value ≤ 1e-100 and identity ≥95%. 5,395 clones were selected and sanger sequenced from 3′ end. of which, 4,915 sequences had a phred quality of  ≥20. we applied 19,532 5′ ests and 4,915 3′ ests to seqclean (http://sourceforge.net/projects/seqclean/), which validates and trims dna sequences. then, 19,487 5′ ests and 4,480 3′ ests were assembled by cap3 with the following parameters (mindistance […]

2017
PMCID: 5423905
PMID: 28539927
DOI: 10.3389/fpls.2017.00694

[…] foundation grants ios-1238142 (ps) and ios-1547787 (wb)., we thank dr. dan nettleton for technical assistance with the sqtl analysis., http://www.maizecdna.org/ , https://sourceforge.net/projects/seqclean/ , http://broadinstitute.github.io/picard/ , https://transdecoder.github.io/ , http://seaborn.pydata.org/generated/seaborn.clustermap.html , http://blast.wustl.edu , […]

2017
PMCID: 5496360
PMID: 28673252
DOI: 10.1186/s12864-017-3897-x

[…] genomics center at the college of agriculture “luiz de queiroz” of the university of são paulo., the adapter sequences and low complexity reads were removed in an initial data-filtering step using seqclean software (https://sourceforge.net/projects/seqclean/files/). the fastqc software was used to analyze the quality of raw reads (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). […]

2017
PMCID: 5725652
PMID: 29228974
DOI: 10.1186/s13104-017-3018-6

[…] high-quality fragments were pooled for de novo transcriptome assembly using trinity v2.2.0 [] producing 149,545 transcripts. several filtration procedures were performed to clean up the assembly: seqclean was used to trim poly-a tails and remove 38 low complexity sequences []. custom scripts were used to remove 745 fragments smaller than 200 bp. back-mapping of input sequencing reads […]

2017
PMCID: 5751233
PMID: 29210992
DOI: 10.3390/ijms18122630

[…] 2.5.3, 454 life sciences, roche, basel, switzerland) at quality score threshold 40 and quality-trimmed with lucy software (version 2.19; available online: http://lucy.sourceforge.net/) [] and seqclean (version 1.0; available online: http://compbio.dfci.harvard.edu). the resulting sequence reads were assembled de novo using the software package newbler (a) set to extend low-depth overlaps. […]


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SeqClean in publications

 (251)
PMCID: 5943399
PMID: 29743478
DOI: 10.1038/s41398-018-0107-9

[…] of reads may affect microbial profiling, we performed normalization by sub-sampling to 100,000 reads for each sample. next, we filtered out low-quality and low-complexity reads using fastx and seqclean (see urls). finally, the remaining reads were realigned to the human references using the megablast aligner in order to exclude any potentially human reads. the remaining reads were used […]

PMCID: 5758534
PMID: 29354108
DOI: 10.3389/fmicb.2017.02622

[…] exact duplicates (possible artifacts from emulsion pcr) using cd-hits (li and godzik, ), and low-quality parts (phred quality < 25, n content > 3%, sequences < 100 bp) were trimmed using seqclean (http://seqclean.sourceforge.net). after quality control, a total of 569,349 metagenome reads and 483,241 metatranscriptome reads (both with average length > 300 bp) were used […]

PMCID: 5798812
PMID: 29423231
DOI: 10.1038/s41438-017-0012-z

[…] remaining high quality reads were filtered for short reads below 50 bp. adaptors were first trimmed, and then reads were further assembled by gs de novo assembler (v2.6). singletons cleaning using seqclean and lucy with a parameter of minimum length 100 bp illumina hiseq reads produced in paired-end formats (101 bp) were also assembled using the trinity software package. reads were filtered […]

PMCID: 5938196
PMID: 29311425
DOI: 10.1292/jvms.17-0448

[…] for downstream analysis. the assembled contigs were subjected to left over adapters and contaminant filter against ncbi univec database via seq clean (default parameter) (http://hpc.ilri.cgiar.org/seqclean/seqclean). the whole genome sequencing project has been submitted to the genbank database (accession no: mwvg00000000)., analyses to determine average nucleotide identity (ani) [] […]

PMCID: 5741957
PMID: 29273003
DOI: 10.1186/s12863-017-0584-5

[…] annotations against egms (fig. and additional file : table s6)., a total of 209,835 tigr transcripts drests and 10,619 unigene clusters (additional file : table s1) were cleaned by a program called seqclean and then aligned to the sorghum genome using the pasa pipeline. the main input parameter for seqclean was a transcript fasta file, but with the vector sequence database, the cleaning process […]


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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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