Tools to detect synteny blocks regions among multiple genomes
...ne conserved synteny blocks. It reconstructs synteny blocks between pairwise comparison of multiple genomes. The reconstructed synteny blocks may overlap each other, be included in on...2604 days ago
String graph based genome assembly software and tools !
...oubleshoot an assembly if it runs into problems. 2. SAGE: String-overlap Assembly of GEnomes http...most assemblers, which are de Bruijn graph based, SAGE uses the string-overlap graph. SAGE builds upon great...2323 days ago
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R Graphical Cookbook by Winston Chang
...ted for each figure is self-contained, i.e., all code required to produce the figure is included. This means that there is sometimes considerable overlap of code between several figur...2148 days ago
Genome Assembly Tools and Software - PART2 !!
...Assembly of GEnomesSAGE is a new string-overlap graph-based de novo genome assembler. Omega 1.0.2 – Overlap-graph de novo Assembler for M...es in an attempt to obtain all sequences that overlaps, directly or indirectly, wit...2680 days ago
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List of In-silico Binding Site Prediction Tools
...as considered a true-positive if the predicted pocket had at-least 10% overlap with the actual ligand. The p...are in the first rank itself. 77% of the predictions had at least 50% overlap with the experimentally obser...3738 days ago
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Tadpole is 250x faster than SPADes assembler !
...te: Shave and rinse can produce substantially better assemblies for low-depth data, but they are very slow for large metagenomes. Overlap parameters (for overlapping paired-end reads only):...970 days ago
Raku script to find overlaps between two bed files !
...$start1 = @fields1[1]; my $end1 = @fields1[2]; # Check for overlaps with intervals in the second...my $end2 = @fields2[2]; # Check for chromosome match and overlap if $chr1 eq $chr2 &&...89 days ago
Tags: multiprocess, distributed, memory, overlap, layout, consensus, OLC, metagenome, assembler
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Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
...put results. Options are: sam - Standard SAM output (in normal and '-w overlap' modes). m5 - BLASR M5 format...re: illumina - Equivalent to: '-a gotoh -w normal -M 5 -X 4 -G 8 -E 6' overlap - Equivalent to: '-a anchor -...2286 days ago