Optimal Syntenic Layouter

|| Summarizing Matches ||

Minimal Match Size: Every sequence match smaller than this value will be removed from the view. Hint: Use this filter if a lot of noise matches appear in the Original Data view which might complicate the computation. [~100-500 bp]
Maximal Distance to Contig Border: Only summarized matches lying within this distance give rise to a connector and therefore can be locally extended. Hint1: If fewer connectors and matches appear in the Summarized Matches view as you have expected, try to increase this value. Hint2: In some cases, decreasing this value might facilitate the computation of a contig layout because the number of false-positive connectors is reduced. [~1000-15000 bp]
Width of Diagonal Search Space: Longer stretches of similar DNA sequences in the dot-plot usually consist of a bunch of seperated, short BLAST matches. These match clusters are substituted by a one-piece diagonal for easier handling. Only BLAST matches found within a imaginary diagonal search space get summarized. Hint: If summarized matches appear to be shorter than the corresponding BLAST matches in the Original Data view, increase this value to extend the search space. [~4000-15000 bp]
Maximal Gap Length between Consecutive Matches: Sequence matches which previously were positioned within a diagonal, now are succeedingly traversed trying to elongate the summarized match as much as possible. However, if the gap length between two consecutive matches is too large, the traversing stops and the summarized match ends at that position. Hint: If summarized matches appear to be shorter than expected, increase this value. [~10000-20000 bp]

|| Contig Layout ||

Maximal Height Difference between Connectors: Only connectors coming from different contigs and lying within this distance can be connected. Hint: This value represents the permitted gap size between two contigs. Be careful when choosing large values: they might bias the result since short contigs originally positioned between these two contigs, could be skipped. [~2000-30000 bp]
Trim Unmatched Contig Ends: Due to inserts of foreign DNA in only one genome for instance, unmatched contig ends (grey region in picture) appear. They often bias the positioning of connectors i.e. calculation of the point where a match would touch the contig border. This option allows you to ignore these unmatched end regions and thereby might advance contig border connections. Hint: This option is useful for genomes containing known inserts, normaly "breaking" contigs into parts. This is observable, when matches do not touch the contig border but end within the contig without giving rise to a connector.
Filter Repeats: Summarized Matches starting or ending at nearly the same coordinates (x and y axis) get removed. If there is only a partial repeat, the longer match is kept. Hint: Removing of repetetive regions located near contig borders can facilitate the layout process because it eliminate unwanted connectors.
Avoid Weak Extensions: Contig ends might contain short match segments which align to other regions than the rest of the target contig. If these short segments give rise to connectors, this can mislead the layout process. This option only keeps the connector derived from the longest marginal match. Others are removed.
Show Only Cells containing Recombinations: If checked, only contigs are shown containing "broken" matches. Considering only single cells respectively, these are matches lying to far apart from each other and/or showing different slopes. Hint: This option does not modify the contig layout! It just keeps the concerned cells visible whereas the others are hidden. It gives the user the possiblity to check whether recombinations or misassemblies exist.
Compute Layout for xAxis (rather than yAxis): If checked, only the vertical (green) connectors are used for computing a layout for the xAxis assembly. If unchecked, only the horizontal (red) connectors are used for computing a layout for the yAxis assembly.
Compute Layout for Both Axis: If checked, both axis are sorted and oriented subsequently. The layout computation of one axis is totally independent from the other axis. If unchecked, only one axis is layouted.
Export Syntenic Layout: If checked, a window appears providing several possibilities to write results to files. List of Supercontigs List of Gap Distances List of Mapped Contigs Supercontig Sequences Rearranged ACE File for Consed

• List of Supercontigs
  OSLay writes a file containing a list of the sorted and oriented contig names.
  The file is named supercontigsList.#.txt where '#' is substituted with x or y depending on which axis was layouted. Ordering both axis in one run generates two files.

  A typical file would look like this:

  1 (4) Contig1* Contig5* Contig2 Contig3*
  2 (3) Contig4 Contig6* Contig7*
  ...
  This example shows 2 supercontigs (indicated by line numbers).
  The first supercontig contains 4, the second supercontig 3 contigs (indicated by numbers in parenthesis)
  The concatenated '*' means that the contig was flipped i.e. it changed its orientation.
  This information is also available in the message window.

• List of Gap Distances
  OSLay is able to predict gap distances between succeeding contigs by measuring the connector height difference of the two concerned contig sides which are neighbored in the contig layout. These distances can be helpful when designing primers on both contig ends (e.g. within Consed).
  Note that these predicted distances are inferred only from the computed connectors ("Anchor point where a summarized match would touch the contig margin"). Thus, negative distances might represent contig overlappings. Therefore with every negative overlap there comes additional information (in squared brackets) if matches do overlap as well. In this case neighbored contig ends may be merged in the assembly.
  The following image illustrates the three situations:
  
  

  Example:

  Contig10 1825 Contig5
  Contig5 56 Contig74
  Contig74 -613 Contig3 [Matches Overlap: 308bp]
  Contig3 -205 Contig9
  ...

• List of Contig Mappings
  In case the reference sequence is an already finished genome, OSLay is able to print out an ascending list of coordinates where each target contig (and its summarized matches respectively) maps onto the reference sequence.
  Therefore every summarized match gives rise to a single record in this list. Thus, contig ids may appear more than once in this list since matches can be distributed in a single contig sequence. A record has the following format:

  <target contigID> --> <start ref genome> <stop ref genome> <[length]> <reverse-complemented>

  Example:

  Contig3 --> 409 7800 [7391] *
  Contig107 --> 511 1246 [735]
  Contig_066 --> 8872 11002 [2130] *
  ...

• Supercontig Sequences
  If checked, a multifasta file is written containing the correctly sorted and oriented contig sequences plus the remaining contigs as DNA sequence. Each supercontig sequence is represented as one entry in the fasta file. The gap distances between contigs within every supercontig are filled with N's depending on the connector height difference.
  The file is named supercontigSequences.#.fna where '#' is substituted with 'x' or 'y' depending on which axis was layouted.

• Rearranged ACE file for Consed
  Consed is a widely-used tool for viewing, editing and finishing sequence assemblies.
  OSLay writes a self generated ACE file which assists the user with obtaining primer pairs for neighbored contigs.
  Two options are available:
  • No ACE file available
    OSLay creates a new one.
  • ACE file is already available from previous assembly
    OSLay reads in an existing ACE file which has to be chosen by the user and creates a second, modified ACE file.
  
  Generally, OSLay creates a new ACE file with rearranged and flipped contigs according to OSLay's computed contig layout. (All coordinates e.g. of concerned reads or affected tags are adapted as well.) Opening the rearranged ACE file in Consed and having the list of supercontigs and the list of gap distances at hand, the user is able to easily connect subsequent contigs by a primer pair bridging the gap between them.
  Untouched contigs not being contained in supercontigs, are appended subsequently at the end of the ACE file.
• Export images
  You are able to export your current view to .png, .eps, .svg, .jpg, or .gif files.
  Exported images look better if you antialias them first.

  Every view is resizable:

  1. first select the view by clicking on it so a red frame becomes visible
  2. press Ctrl and at the same time drag the nodes at the corners
  
  If you want to hide certain views check these options. Maybe you want to change the background color of the window.

• Saving .cgv files
  To not being asked to import all files and to readjust all parameter again when restarting OSLay, you can save your results and configurations in a .cgv file.
  Therefore select File > Save > View and Data... and choose a file name.
  All data plus your current views are saved so you do not have to import the raw data again.
• Opening .cgv files
  To open a given .cgv file, start OSLay.
  Then select File > Open... and choose your file.