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SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
By Neel 1906 days agogithub.com - 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) expedites sequence alignment calculation for both short...FRODOCK 2.0: fast protein–protein docking server
By Neel 2701 days ago Comments (1)frodock.chaconlab.org - frodock: a user-friendly protein–protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select...SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
By Jit 2277 days agoacademic.oup.com - The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary information on benchmarking procedure as well as test data are publicly accessible at the project documentation...PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
By Rahul Nayak 1419 days agogithub.com - PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish index. PuffAligner is able to produce highly sensitive alignments, similar to those of Bowtie2, but much more quickly. While exhibiting similar speed to the ultrafast...Termal: a fast and interactive terminal-based viewer for multiple sequence alignments
By LEGE 169 days agogithub.com - termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC)...Cerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 2835 days agosourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in...
Evaluation of genome assembly software based on long reads
By BioStar 2594 days agoTGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence...LncPipe:A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq...
By LEGE 1635 days agogithub.com - The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3282 days agoStructural variation caller tools using long readsMafTools
By Jit 3309 days agogithub.com - maftools - An R package to summarize, analyze and visualize MAF files. Introduction. With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widley accepted and used to store variants detected. The Cancer Genome Atlas Project...
