LAMSA: fast split read alignment with long approximate matches
...l split alignment approach with faster speed and good ability of handling SV events. It is well-suited to align long reads (over thousands of base-pairs). LAMSA takes takes the ad...2197 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
...compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural featu...2189 days ago
2183 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
...y (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial...re, it is useful for pairwise ANI computation of large number of genome pairs. More details about its speed...2137 days ago
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
...ave money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store only those read-pairs or reads who intersect some r...2054 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
...single transitive links (single linkage) with alignment coverage constraints. SiLiX adopts a graph-theoretical framework to interpret similarity pairs as edges of a network. A very...1985 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
...d an associated haplotig. This can be an issue for downstream analysis whether you're working on the haploid or phased-diploid assembly. Identify pairs of contigs that are syntenic...1981 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
...The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorith...R tries to identify PBS, PPT and RT inside LTR pairs by build-in aligning and coun...1954 days ago
FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
...notyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human geno...1574 days ago
1397 days ago