SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists
...uding Windows XP SP3 32bit, Windows Vista 32bit, Windows 2008 Server, Windows 7 32bit and 64bit, Ubuntu 10.04 64bit, Ubuntu 10.10 64bit, and gentoo AMD64. The corresponding publica...2353 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...nd then count how many contigs: grep ">" reads.fa | wc -l # Download sample PacBio from the PBcR website wget -O- http://www.cbcb.umd.edu/software/PBcR/data/selfSa...2349 days ago
2347 days ago
alienness : Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life
...particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr http://www.mdpi.com/2073-4425/8/10/248...2244 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error corre...2184 days ago
minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.2171 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
...hromosome-scale assembly. bioRxiv, p.261149 Link For any queries, please either ask on github issue page or send an email to Jay Ghurye (jayg@cs.umd.edu).2149 days ago
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
...ace that allow researchers to calculate OrthoANI values between genomes of interest without unfamiliar Command Line Environments. Moreover, the OAT_cmd command-line software can be...1969 days ago
HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of...1949 days ago
1939 days ago