Genome analysis

• OPERA-MS: Hybrid Metagenomic Assembler

genome assembly hybrid assembly metagenomic illumina nanopore pacbio
• A hybrid metagenomic assembler which combines the advantages of short and long-read technologies to provide high quality assemblies, addressing issues of low contiguity for short-read only assemblies, and low base-pair quality for long-read only assemblies.

GitHub: User manual and software

• LoFreq: High Sensitivity Variant Caller

variant caller cancer metagenomic
• SNPs+Indels, Fast, Rare variants (<1%)

GitHub: User manual and software

SourceForge: Download software

• OPERA-LG: Genome Scaffolder

genome assembly metagenomic nanopore pacbio
• Robust & Efficient, Handles Repeats, Matepairs+Long-reads

Wiki: User manual

SourceForge: Download software

• INC-Seq

high accuracy rolling circle amplification nanopore pacbio
• Accurate single molecule reads using nanopore sequencing

GitHub: User manual and software

• GraphMap

mapper nanopore pacbio
• A highly sensitive and accurate mapper for long, error-prone reads

GitHub: User manual and software

• Racon

consensus de novo assembly nanopore pacbio GPU
• Consensus module for raw de novo DNA assembly of long uncorrected reads.

GitHub: User manual and software

• PORE-cupine

isoform-specific RNA structure nanopore
• Chemical utilized probing interrogated using nanopores

GitHub: User manual and software

• miniBarcoder

DNA barcoding nanopore MinION
• A MinION‐based pipeline for fast and cost‐effective DNA barcoding

GitHub: User manual and software

• GiRaF

reassortments influenza
• Robust, Computational Identification of Influenza Reassortments via Graph Mining

GitHub: User manual and software

Metagenomic system biology

• BEEM: microbial community dynamics

microbial interactions metagenomic longitudinal data gLVM
• Modelling microbial community dynamics based on longitudinal metagenomic sequencing data (16S or shotgun-metagenomics). It is based on the commonly used generalized Lotka-Volterra modelling (gLVM) framework.

GitHub: User manual and software

• BEEM-static

microbial interactions metagenomic gLVM
• Learning directed microbial interactions from cross-sectional microbiome profiling data based on the generalized Lotka-Volterra model (gLVM).

GitHub: User manual and software

• @MInter

microbial interactions SVM
• SVM/regex abstract parser for identification of microbial interactions

GitHub: User manual and software

• PLoT-ME

metagenomic taxonomic classification memory efficient nanopore pacbio
• Pre-classification of Long-reads for Memory Efficient Taxonomic assignment

GitHub: User manual and software

Cancer genomics

• TUGDA

cancer drug response prediction domain adaptation gene expression
• Task uncertainty guided domain adaptation for robust generalization of cancer drug response prediction from in in vitro to in vivo settings

GitHub: User manual and software

• OncoIMPACT

cancer driver prediction multiomics gene expression mutation
• OncoIMPACT is a first-in-class algorithmic framework that nominates patient-specific driver genes by integratively modeling genomic mutations (point, structural and copy-number) and the resulting perturbations in transcriptional programs via defined molecular networks.

GitHub: User manual and software

• CaDRReS

cancer drug response prediction pharmacogenomic gene expression
• Cancer Drug Response prediction using a Recommender System (CaDRReS) is based on the matrix factorization approach to predict which drugs are sensitive for an unseen cell line.

GitHub: User manual and software

• CaDRReS-Sc

tumor heterogeneity drug response prediction pharmacogenomic scRNA-seq gene expression
• A framework for analyzing drug response heterogeneity based on single-cell RNA-seq data

GitHub: User manual and software

Others

• EDDA

differential abundance experimental design
• Experimental Design in Differential Abundance analysis (EDDA) is a tool for systematic assessment of the impact of experimental design and the statistical test used on the ability to detect differential abundance.

GitHub: User manual and software