Etool support - Sibelia support channel

 At 2013-10-04 08:54:48 AM - 

Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes.

Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham. Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes.

Sibelia will be presented at 13th Workshop on Algorithms in Bioinformatics (WABI2013) in Nice, Sophia Antipolis, France.

Arxiv version is available: http://arxiv.org/abs/1307.7941

If you have any question of running this tool or any suggestion please feel free to ask in this channel. 

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Sibelia 3.0.4

 At 2013-10-04 08:54:48 AM

Release date: 3rd October 2013

Authors
  • Ilya Minkin (St. Petersburg Academic University)
  • Nikolay Vyahhi (St. Petersburg Academic University)
  • Mikhail Kolmogorov (St. Petersburg Academic University)
  • Ekaterina Starostina (St. Petersburg Academic University)
  • Son Pham (University of California, San Diego)

Introduction

This package contains two programs:

  • Sibelia -- "Sibelia" is a tool for finding synteny blocks in closely related genomes, like different strains of the same bacterial species. It takes a set of FASTA files with genomes and locates coordinates of the synteny blocks in these sequences. It also represents genomes as permutations of the blocks.

  • C-Sibelia -- This tool is designed for comparison between two genomes represented either in finished form or as sets of contigs. It is able to detect SNPs/SNVs and indels of different scales. "C-Sibelia" works by locating synteny blocks between the input genomes and aligning different copies of a block. It considers only unique blocks, i.e. blocks having one copy in reference and one copy in another genome. It is also possible to get the alignments itself, in this case you will get the alignments of repeats within genomes as well.

It also contains a script for annotation of variants found by "C-Sibelia" using the "snpEff" tool.