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Sibelia specifications

Information


Unique identifier OMICS_11719
Name Sibelia
Alternative name Synteny Block ExpLoration tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sibelia takes a set of FASTA files with genomes.
Output data It locates coordinates of the synteny blocks in these sequences. It also represents genomes as permutations of the blocks.
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.0.6
Stability Stable
Requirements
Ibdivsufsort, TCLAP, Boost, D3.js, Seqan
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Nikolay Vyahhi

Publication for Synteny Block ExpLoration tool

Sibelia citations

 (9)
library_books

Genome rearrangements and phylogeny reconstruction in Yersinia pestis

2018
PeerJ
PMCID: 5877447
PMID: 29607260
DOI: 10.7717/peerj.4545

[…] Synteny blocks were constructed using the Sibelia algorithm () with the block length threshold 5,000 bp. To ensure robustness of the tree topology relative to this parameter we also performed calculations with the block length thresholds of 5 […]

library_books

Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus

2017
Sci Rep
PMCID: 5374712
PMID: 28361960
DOI: 10.1038/srep45771

[…] (version 1.1) was used to call variants from reads having a mapping quality of at least 20.The variants among the 45 complete genomes (including the used reference genome) were identified by using C-Sibelia (version 3.0.5) with default parameters. […]

library_books

Patterns and Processes of Mycobacterium bovis Evolution Revealed by Phylogenomic Analyses

2017
Genome Biol Evol
PMCID: 5381553
PMID: 28201585
DOI: 10.1093/gbe/evx022

[…] Sibelia () was used to assess chromosomal structural variations across the five M. bovis complete genomes (excluding BCG genomes, as these do not represent natural genomic variation) present in NCBI’s […]

library_books

Approaches for in silico finishing of microbial genome sequences

2017
Genet Mol Biol
PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] e URL http://bioen-compbio.bioen.illinois.edu/RACA/.Ragout (): uses phylogenetic information and synteny blocks to order a set of contigs from a target genome using multiple genome references. First, Sibelia () is used to identify synteny blocks shared by the target and the reference sequences. Based on the synteny, the nucleotides of the genomes are represented as sequences of blocks, and the bes […]

library_books

LRR RLK family from two Citrus species: genome wide identification and evolutionary aspects

2016
BMC Genomics
PMCID: 4982124
PMID: 27515968
DOI: 10.1186/s12864-016-2930-9

[…] The synteny analyses were performed using Sibelia software. Although this tool was originally optimized to efficiently identify syntenic blocks between closely related microbial genomes [], this tool was employed because the chromosome compar […]

library_books

VGSC: A Web Based Vector Graph Toolkit of Genome Synteny and Collinearity

2016
Biomed Res Int
PMCID: 4783527
PMID: 27006949
DOI: 10.1155/2016/7823429

[…] n be created from GFF-style data inputs and hierarchical configuration files, which are popular in bioinformatics researches, making Circos suitable for rapid reporting pipelines. A typical case is C-Sibelia [], which focuses on the synteny and collinearity analysis and outputs the Circos-formated file to plot. Many recent genetic research reports in Nature and Science have applied Circos-styled f […]

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