Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...ov Model with respect to the underlying platformtextquoterights error profile. The algorithm learns a posterior transition/emission probability distribution for each long read and uses t...2078 days ago
SimLoRD: A read simulator for third generation sequencing reads
...ion of genome rearrangements may be incorporated at a later stage.) The read lengths can be determined in four ways: drawing from a log-normal distribution (typical for genomic DNA), sa...2076 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
...user interface, that can also be executed via command line. CSBFinder implements a novel methodology for the discovery, ranking, and taxonomic distribution analysis of colinear syntenic...2013 days ago
2001 days ago
RepeatMasker compatible blast tool
RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn...1969 days ago
PilonGrid: parallel wrapper around the Pilon framework
The distribution is a parallel wrapper around the Pilon framework The pipeline is composed of bash scripts, an example mapping.fofn which shows how to input your fastq files (you give paths to the R1 file), and how to launch the pipeline.1963 days ago
1924 days ago
1923 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
...for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a distribution of proportion of bases covere...1625 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
...n a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered around parsimonious...1577 days ago