alien_index : identify potential contaminants or horizontally transferred genes in transcriptomes.
identify potential contaminants or horizontally transferred genes in transcriptomes. algorithm is based on alogorithm described in the following: Gladyshev, Eugene A.,...1546 days ago
MEC: Contig Misassembly Correction
MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a...1543 days ago
1531 days ago
SvABA: Structural variation and indel detection by local assembly
...eads at the command line using VariantBam rules. These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants. Sequencing reads ar...1509 days ago
1512 days ago
Mercator: Multiple Whole-Genome Orthology Map Construction
Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple gen..., and "paralogous" instead. Ideally, given K genomes, we would like to identify all orthologous genomic regio...1439 days ago
PhiSpy: PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes
PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes. Given an annotated genome it will use several approaches to identify the most likely prophage regions. Initia...1397 days ago
PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes
...ral task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use recipro...are computationally expensive, requiring O(n2) resources to identify RBHs. This is problematic, as...1353 days ago
proActiv: Estimation of Promoter Activity from RNA-Seq data
...iv uses aligned reads and genome annotations as input, and provides absolute and relative promoter activity as output. The package can be used to identify active promoters and alternat...1353 days ago
mixtureS: a novel tool for bacterial strain reconstruction from reads
mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on...1345 days ago