Software
Here you can find a list of software and research topics that I am currently interested in.
Most of the software are available on my repository on github.
Genotyping :
- VG SNP-Aware: Fast Alignment of Reads to a Variation Graph with Application to SNP Detection
VG SNP-Aware - GenoLight: Indexing K-mers in Linear Space with Applicationto SNP Detection
GenoLight
Alignment-Free Measures
- Alignment-free comparison of regulatory sequences (cis-regulatory modules)
UnderII - regulatory sequences comparison - Assembly-free Genome Comparison based on Next-Generation Sequencing Reads and Variable Length Patterns
Assembly-free Genome Comparison - QCluster: Extending Alignment-free Measures with Quality Values for Reads Clustering
QCluster - Alignment-free genome comparison based on Sequencing Reads and Quality Values
c2q
MetaGenomics
- MetaProb: Accurate Metagenomics Sequence Classification based on Probabilistic Sequence Signatures
MetaProb - Higher Recall in Metagenomic Sequence Classification Exploiting Overlapping Reads
CLIOR - Metagenomic reads binning with spaced seeds
MetaProbS - SKraken: Fast and Sensitive Classification of Short Metagenomic Reads based on filtering uninformative k-mers
SKraken - MetaCon: Unsupervised Clustering of Metagenomic Contigs with Probabilistic k-mers Statistics and Coverage
MetaCon - K2MEM: Improving Metagenomic Classification using discriminative k-mers from sequencing data
K2MEM - MetaProb 2: Improving Unsupervised Metagenomic Binning with Efficient Reads Assembly using Minimizers
MetaProb2 - ClassGraph: Boosting Metagenomic Classification with Reads Overlap Graph
ClassGraph
Sequence Entropy
- Fast Computation of Entropic Profiles for the Detection of Conservation in Genomes
Fast Entropic Profiler - EP-sim: Multiple-resolution alignment-free measure based on Entropic Profiles
EP-sim
Phylogenetic
- Ultrametric Networks: A New Tool For Phylogenetic Analysis
Ultranet
String Hashing
- Fast Spaced Seed Hashing
FSH - Fast Indexing for Spaced-seed Hashing
FISH - Iterative Spaced Seed Hashing
ISSH
Pattern Discovery:
- Varun: Extensible motif discovery
Varun - Subtle Motif Finder: Detection of consensus motifs.
www.research.ibm.com/computationalgenomics
Pattern Filtering
- Alignment-Free Phylogeny of Whole Genomes using Underlying Subwords
Underlying Subwords - Filtering Degenerate Motifs with Application to Protein Sequence Analysis
Pattern Filtering
Data Compression
- YALFF (Yet Another Lossy FASTQ Filter): quality score compression through sequence-based quality smoothing
YALFF