Assembly Converter protocols

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Assembly Converter specifications

Information


Unique identifier OMICS_15151
Name Assembly Converter
Interface Web user interface
Restrictions to use None
Input format BED, GFF, GTF, WIG, VCF
Computer skills Basic
Stability Stable
Maintained Yes

Assembly Converter in pipeline

2015
PMCID: 4587370
PMID: 26451251
DOI: 10.1038/sdata.2015.51

[…] in this study (see data citation 1 ), researchers must update it to the most updated genome version using the liftover software from ucsc (https://genome.ucsc.edu/cgi-bin/hgliftover) or the assembly converter from ensembl (http://www.ensembl.org/homo_sapiens/tools/assemblyconverter)., software used during this study went through minor and major code base updates. the more notable […]


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Assembly Converter in publications

 (8)
PMCID: 5741965
PMID: 29272997
DOI: 10.1186/s12864-017-4351-9

[…] from the grch38 human assembly to the rat rgsc-3.4 assembly using mapping from grch38 to rno6.0 and then from rno6.0 to rno5.0 and rgsc-3.4. all conversions used the ensembl perl api and the ensembl assembly converter software (v87 []). as with other genetic elements analysed, we then used permutation tests to determine if there was a significant enrichment of rat orthologous positions […]

PMCID: 5633198
PMID: 28953891
DOI: 10.1371/journal.pgen.1007019

[…] obtained from snpeff []. the multi-species alignment made use of the b73 agpv3 assembly, and to ensure consistent coordinates, we ported our snp coordinates from agpv2 to agpv3 using the gramene assembly converter (http://ensembl.gramene.org/zea_mays/tools/assemblyconverter?db=core)., to compare gerp scores (for all snps with gerp > 0) to recombination rate and allele frequencies, […]

PMCID: 5522596
PMID: 28732548
DOI: 10.1186/s13059-017-1273-4

[…] tes and cnss were selected and counted using bedtools []. the cns coordinate data were extracted from published rice v6 versus maize v2 data [] and the coordinates were converted from v2 to v4 using assembly converter available on ensembl plants []., te annotations are available at the gramene database (ftp://ftp.gramene.org/pub/gramene/current_release/data/gff3/zea_mays/repeat_annotation/) [] […]

PMCID: 5417718
PMID: 28472114
DOI: 10.1371/journal.pone.0177014

[…] in this study and the genome-wide association study (gwas) regions described in ramayo-caldas et al. [] using bc1_ld animals of the ibmap population. after remapping these regions using the assembly converter tool of ensembl, 19 regions co-localized among these works (). the overlapping between the cnvrs and qtls for growth and body composition traits described in fern├índez et al. [], […]

PMCID: 4973992
PMID: 27490364
DOI: 10.1371/journal.pgen.1006178

[…] [] to predict the effect of snps in protein function []. the current version of ensembl vep uses rat genome rnor_6.0 assembly, we therefore convert our data from rnor_5.0 to rnor_6.0 using ensembl assembly converter (http://useast.ensembl.org/common/tools/assemblyconverter) before uploading data to vep. to predict the effects of promoter ss on altering putative transcription factor binding, […]


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