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High Throughput sequencing
- mrFAST: Read mapper developed
specifically for structural variation and segmental duplication
detection using the Illumina platform. Supports small indel
- mrsFAST: Similar to mrFAST, Hamming
Read depth analysis method to characterize segmental
duplications and predict absolute copy numbers.
Tool to efficiently compress FASTQ files.
Toolkit for automatic and rapid discovery of structural variants.
Discovery and genotyping of novel sequence insertions in many
Discover inversions using long range information -- linked-read
FPGA design for accelerating pre-alignment in DNA short read
GPGPU design for accelerating pre-alignment in DNA short read
FPGA-based filtering strategy with high accuracy across different
edit distance thresholds.
Fast and efficient computation of banded sequence alignment.
Approximate alignment computation on CPU, GPU, and FPGA by reducing
alignment problem to single net routing problem.
Profile HMM-based hybrid error correction algorithm for long reads.
Profile HMM-based genome assembly polishing tool.
Discovery of mid range novel sequence insertions using long-read
CNV prediction polisher on whole exome sequencing data.
approximate string matching (ASM) acceleration framework for genome sequence analysis.
universal genomic mapping accelerator that supports both sequence-to-graph mapping and sequence-to sequence mapping, for both short and long reads.
Tool for quickly remapping reads between genome assemblies.
Fast, memory-efficient, and accurate mechanism to find fuzzy seed matches in genome analysis.
Fast and comprehensive technique for translating alignments between reference genomes.
Pre-basecalling filter for nanopore sequencing.
A software tool that processes and manipulates multiple
alignments of genomic sequences.
Characterization of segmental duplication evolutionary structure
across genome assemblies.
Tool designed to detect specialized hubs among the proteins providing cell-to-cell interactions in protein-protein interaction networks that include the proteins of two interacting cells.
High Throughput Sequencing
- drFAST: Read mapper for di-base
color-space reads generated with the SOLiD platform.
- sirFAST: Read mapper for short
interrupted reads generated with the Complete Genomics platform.
Structural variation calling algorithm using read pair mapping
information including suboptimal alignments. (replaced by TARDIS)
Detection of structural variants and indels from genome and
exome sequencing data.
Novel sequence insertion discovery framework. (replaced by Pamir)
Discover inversions using long range information.(replaced by VALOR2)
- taveRNA suite
Algorithm that predicts the joint secondary structure of
two RNA sequences.
Densityfold algorithm that
minimizes a linear combination of energy density and the
total free energy.
RNA interaction search engine. pRuNA is a sequence based
pruning technique that eliminates a significant fraction of a non
coding RNA (ncRNA) data set and retains only the most likely ncRNA
candidates for forming a stable joint structure with the query
- piRNA: RNA-RNA interaction
partition function algorithm to predict the joint partition
function, equilibrium concentration, ensemble energy, and melting
temperature for two RNA sequences.
Novel ab initio
non-coding RNA finder.
An ab initio centromeric
sequence detection algorithm.
Characterization of segmental duplications within genome assemblies. (replaced by BISER)