LookSeq protocols

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Associated diseases

Associated diseases

LookSeq specifications

Information


Unique identifier OMICS_00886
Name LookSeq
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Heinrich Magnus Manske <>

Publication for LookSeq

LookSeq in pipeline

2016
PMCID: 5087946
PMID: 27798646
DOI: 10.1371/journal.pntd.0005091

[…] we used bwa [] to map previously-generated illumina sequence reads from individual cambodian p. vivax isolates to the sal1 reference genome []. visual inspection of the alignments in artemis [] and lookseq [] clearly showed increased sequence coverage at the pvdbp locus in some isolates, including some where pcr-based detection had failed. isolate pv0431 showed increased sequence coverage […]


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LookSeq in publications

 (11)
PMCID: 5259787
PMID: 28117431
DOI: 10.1038/srep41303

[…] and subsequently increased in frequency to represent more than 20% of the mapped sequence reads. the quality of the mapped sequence reads for each of these cases were inspected visually using the lookseq software. to compare with the sequences in long-term laboratory adapted strains, a global dataset of clinical p. falciparum samples was examined, using the pf3k project release 3.1 […]

PMCID: 5389722
PMID: 27994033
DOI: 10.1093/nar/gkw1259

[…] rank sum tests (discussed further in ))., we used samtools mpileup followed by bcftools () to detect bps, exactly as described previously (), and confirmed all variants by manual inspection on lookseq (). as expected, larger clone trees (with more subclone genomes analysed and longer in vitro culture times) yielded more de novo bps than smaller ones ()., we used genome analysis toolkit […]

PMCID: 5087946
PMID: 27798646
DOI: 10.1371/journal.pntd.0005091

[…] present study, the resulting assembly bam files were reviewed in the region containing pvdbp (chromosome 6: 976329–980090, genbank accession id = pvx_110810) using the artemis genome viewer [] or lookseq []. mate pairs that were oriented tail-to-tail, and thus signified that pvdbp was duplicated, were visualized in either artemis using a “non-proper pair” read filter or lookseq using […]

PMCID: 4270465
PMID: 25521112
DOI: 10.1371/journal.pgen.1004812

[…] mapping quality >25, reject bi- or tri-allelic calls, at least 5 non-ref reads, number ref reads less than 20% of all reads. from this output list, each potential snp was then visualised on lookseq , an online tool in which sequence coverage is represented by a pile-up of blue reads matching the 3d7 reference genome, with mismatches in red. finally, 95% of all detected snps had maximal […]

PMCID: 4086683
PMID: 24963649
DOI: 10.1038/ncomms5248

[…] individuals were re-checked for read depth, particularly in regions of interest, and molecular form was validated in the genome sequence data via presence/absence of the sine insertion using lookseq., genomic divergence between mosquito sample groups and pairwise nucleotide diversity within groups were calculated for every snp using vcftools version 0.1.9.0 (ref. ) (commands) via […]


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LookSeq institution(s)
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
LookSeq funding source(s)
Supported by the Wellcome Trust, the Bill and Melinda Gates Foundation, and the Medical Research Council.

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