Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compi...1611 days ago
3D de novo assembly (3D DNA) pipeline
For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aidenlab.org...1605 days ago
Musket - a multistage k-mer spectrum based corrector
Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spe...1603 days ago
ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been optimize...1560 days ago
Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.
Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library. Please see Achieving Success with De Novo Assembly and ...1487 days ago
1448 days ago
RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types: single-end/paired-en...1448 days ago
mixtureS: a novel tool for bacterial strain reconstruction from reads
mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. T...1405 days ago
1401 days ago
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, on...1280 days ago