LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
LR_Gapcloser is a gap closing tool using long reads from studied species. The long rea...our own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the packag...1478 days ago
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxon...n microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gen...1474 days ago
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The wavefront alignment (WFA) algorithm
The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage ofhomologous regions between the sequenc...gnment process. As opposed to traditional dynamic programming algorithms that run in quadratic time,...1433 days ago
ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome bac...1418 days ago
RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
RosettaAntibodyDesign (RAbD) is a generalized framework for the design of antibod...s, in which a user can easily tailor the run to their project needs. The algorithm is meant to sample the divers...1350 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...1310 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...1297 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...1282 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...1259 days ago