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