Official GitHub repository:
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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
alignments.
- mrsFAST: Similar to mrFAST, Hamming
distance only.
- mrCaNaVaR:
Read depth analysis method to characterize segmental
duplications and predict absolute copy numbers.
- SCALCE:
Tool to efficiently compress FASTQ files.
- TARDIS:
Toolkit for automatic and rapid discovery of structural variants.
- Pamir:
Discovery and genotyping of novel sequence insertions in many
sequenced individuals.
- VALOR2:
Discover inversions using long range information -- linked-read
version.
- GateKeeper:
FPGA design for accelerating pre-alignment in DNA short read
mapping.
- GateKeeper-GPU:
GPGPU design for accelerating pre-alignment in DNA short read
mapping.
- MAGNET:
FPGA-based filtering strategy with high accuracy across different
edit distance thresholds.
- Shouji:
Fast and efficient computation of banded sequence alignment.
- SneakySnake:
Approximate alignment computation on CPU, GPU, and FPGA by reducing
alignment problem to single net routing problem.
- Hercules:
Profile HMM-based hybrid error correction algorithm for long reads.
- Apollo:
Profile HMM-based genome assembly polishing tool.
- RinsLR:
Discovery of mid range novel sequence insertions using long-read
sequencing.
- DeCoNT:
CNV prediction polisher on whole exome sequencing data.
- GenASM:
approximate string matching (ASM) acceleration framework for genome sequence analysis.
- SeGraM:
universal genomic mapping accelerator that supports both sequence-to-graph mapping and sequence-to sequence mapping, for both short and long reads.
- FastRemap:
Tool for quickly remapping reads between genome assemblies.
- BLEND:
Fast, memory-efficient, and accurate mechanism to find fuzzy seed matches in genome analysis.
- AirLift:
Fast and comprehensive technique for translating alignments between reference genomes.
- TargetCall:
Pre-basecalling filter for nanopore sequencing.
Others
- MaM:
A software tool that processes and manipulates multiple
alignments of genomic sequences.
- BISER:
Characterization of segmental duplication evolutionary structure
across genome assemblies.
- BriFin:
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.
- SABER:
Tool to perform pairwise sequence alignment using block edits and rearrangements.
- Linden:
Alternating Lyndon Factorization Tree data structure and its application to whole-genome alignments.
Deprecated Tools
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.
- VariationHunter:
Structural variation calling algorithm using read pair mapping
information including suboptimal alignments. (replaced by TARDIS)
- SPLITREAD:
Detection of structural variants and indels from genome and
exome sequencing data.
- NovelSeq:
Novel sequence insertion discovery framework. (replaced by Pamir)
- VALOR:
Discover inversions using long range information.(replaced by VALOR2)
RNA analysis
- taveRNA suite
- inteRNA:
Algorithm that predicts the joint secondary structure of
two RNA sequences.
- alteRNA:
Densityfold algorithm that
minimizes a linear combination of energy density and the
total free energy.
- pRuNA:
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
mRNA.
- piRNA: RNA-RNA interaction
partition function algorithm to predict the joint partition
function, equilibrium concentration, ensemble energy, and melting
temperature for two RNA sequences.
- smyRNA:
Novel ab initio
non-coding RNA finder.
Others
- RepeatNet:
An ab initio centromeric
sequence detection algorithm.
- SEDEF:
Characterization of segmental duplications within genome assemblies. (replaced by BISER)