RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
RosettaAntibodyDesign (RAbD) is a generalized framework for the design of antibo...s, in which a user can easily tailor the run to their project needs. The algorithm is meant to sample the divers...1346 days ago
URMAP, an ultra-fast read mapper
URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calli...1307 days ago
CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R
CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all nece...1294 days ago
MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bo...1279 days ago
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) e...1256 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...competitive with the best assemblers. It also introduces a new graph binning algorithm and achieves the best haploty...1251 days ago
869 days ago
AGORA: Algorithm for Gene Order Reconstruction in Ancestors
AGORA stands for “Algorithm for Gene Order Reconstruction in Ancestors” and was developed by Matthieu Muffato in the DYOGEN Laboratory at the École normale sup&ea...820 days ago
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multipl...786 days ago
JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges
This tool is used to merge structural variants (SVs) across samples. Each sample has...SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of...696 days ago