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SATSUMA : Highly sensitive whole-genome synteny alignments.
...is designed to run on multi-core architectures. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days on 24 CPUs. You can find the manual here. Download the...2913 days ago
- In a nutshell Anvi’o is an analysis and visualization platform for ‘omics data. Please find the methods paper here: https://peerj.com/articles/1319/ Anvi’o would...
2879 days ago
- Decoding SAM flags This utility makes it easy to identify what are the properties of a read based on its SAM flag value, or conversely, to find what the SAM Flag value would be for...
2866 days ago
- ...of a typical assembler, fermi also aims to preserve heterozygotes which are often collapsed by other assemblers. Its ultimate goal is to find a minimal set ofunitigs to re...
2794 days ago
Maq: Mapping and Assembly with Quality
...ndex -i -c consensus.cns all.map; maqview -c consensus.cns all.map Even for advanced maq users, running `maq.pl demo' is recommended. You may find something helpful.2720 days ago
- ...gner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment...ore sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. U...ignments, YAHA uses a directed acyclic graph to find the optimal set of alignments...
2661 days ago
- ...mplementary strand. When mismatches occur in the overlapping region, the base with the better quality score is chosen.The algorithm is as follows:1.Find the positions where the forwa...
2658 days ago
- ...as the data is in MAF format. Maftools can also handle ICGC Simple Somatic Mutation format. maftools is on bioRxiv Please cite the below if you find this tool useful for you. Ma...
2634 days ago
- ...align, order, orientate) , visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions and ident...
2634 days ago
- ...including estimated completeness, GC content and genome size in the binning summary page.Users can use MEGAN or similar software on MaxBin bins to find the taxonomy of each bin afte...
2616 days ago
