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shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other a...1229 days ago
- ...ences Computation Initiative (VLSCI), University of Melbourne. It is based around BWA, GATK and ENSEMBL and was originally designed for human (or similar) data. The master branch is c...
3663 days ago
- NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. I...
3016 days ago
- ...Use sequence quality data properly. Compare DNA to proteins, with frameshifts. Compare PSSMs to sequences Calculate the likelihood of chance similarities between random sequences...
2989 days ago
CovCal: Coverage / Read Count Calculator
...guration and genome size, then select what you want to calculate. Written by Stephen Turner, based on the Lander-Waterman formula, inspired by a similar calculator written by James H...2176 days ago
- ...index (FMD-index) as the key data structure. It is inspired by the string graph assembler (Simpson and Durbin, 2010 and 2012) and has a similar workflow.As a typical de novo...
2805 days ago
- ...s. One of the main challenges in analyzing a metagenome is phylogenetic classification of raw sequence reads into groups representing the same or similar species. Such classification...
2774 days ago
- ...jn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to ot...
2715 days ago
Many-Core Engine (MCE) for Perl example
...E. The author has full control when utilizing this model. MCE::Flow is similar to MCE::Loop, but allows for...change to syntax. MCE::Grep Provides a parallel grep implementation similar to the native grep function....2661 days ago
- ...report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page.Users can use MEGAN or similar software on MaxBin bins to fi...
2627 days ago
