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...2618 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...2336 days ago
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2803 days ago
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...2162 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...2693 days ago
3954 days ago
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...3752 days ago
3893 days ago
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):...984 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 &&...102 days ago
2107 days ago
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 -...2300 days ago