regioneR: an R package for the management and comparison of genomic regions
Regioner is an R package for the management and comparison of genomic regions. It offers a set of function for basic manipulation of region sets extending the functional...ble to study the association of a set of regions with other sets of regions,...1965 days ago
SvABA: Genome-wide detection of structural variants and indels by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wi...ontigs are assembled for every 25kb window (with some small overlap) for every region in the genome. The default is...1924 days ago
HumCFS: a database of fragile sites in human chromosomes
Fragile sites are specific chromosomal region that exhibit an increased frequency of chrom...m the discovery of chromosomal fragile sites/regions (CFS), several line of evide...e is large gap in our knowledge of human CFS region as knowledge about CFS are un...1834 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast...-as would be used for CNV calling.the mean per-region given a BED file of regions.a distribution of proportion...hold output to indicate how many bases in each region are covered at the given thre...1625 days ago
SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wi...ontigs are assembled for every 25kb window (with some small overlap) for every region in the genome. The default is...1510 days ago
Mercator: Multiple Whole-Genome Orthology Map Construction
Whole-genome homology maps attempt to identif..."syntenic" is often used to describe regions of multiple genomes that are...elieved to have evolved from the same region in an ancestral genome. Howev...e to identify all orthologous genomic regions as well as paralogous region...1440 days ago
1431 days ago
DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
The DADA2 tutorial goes through a typical workflow for paired end Illumina M...n both ends of each ITS read, a key step due to the variable length of the ITS region. Short demonstrations of&nbs...1265 days ago
1192 days ago
Kmer: a suite of tools for DNA sequence analysis
More at https://help.rc.ufl.edu/doc/Kmer This also includes: A2Amapper: ATAC, Assembly to Assembly Comparis...d for high-throughput batched alignment. LEAFF: LEAFF (ahem, Let's Extrac...985 days ago