RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
RITA is a standalone software package and Web server for taxonomic assignment of metage...ons for all sequences to be classified, RITA uses a pipeline to first identify cases where both types of classifie...2352 days ago
2339 days ago
HTTDB - Horizontally transferred transposable elements database
Transposons or Transposable elements (TEs) are "mobile genes...nbsp;to D. melanogaster. Since then, many more cases have been documented in the l...T patterns, such as where in the tree of life these cases are more frequently found. Th...2295 days ago
SCUBAT: Scaffolding Contigs Using Blat And Transcripts
SCUBAT (Scaffolding Contigs Using BLAT And Transcripts) uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome.2247 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
Gblocks eliminates poorly aligned positions and divergent regions of a DNA or prot...possible without loosing the functionality that it is necessary in most of the cases. Other options can be changed...2166 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from R...istics for each TE family (number of TE copies, genome coverage...) Ambiguous cases such as nested TE can be asse...2164 days ago
2162 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platforms can lead to tra...including de novo assembly, fusion and structural variation detection. In such cases researchers often combine bot...2086 days ago
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
VariantBam is a tool to extract/count specific sets of sequencing reads from next-gener..., disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient t...2041 days ago
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By...rt of the Thousand Genomes and WGS500 projects, and is being used in clini...2021 days ago