YASS :: genomic similarity search tool
YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BLAST, PATTERNHUNTER, BLASTZ/LASTZ, LAST ...), YASS uses seeds to de...Tags: Bioinformatics, NGS, Alignment, Genome, YASS
2935 days ago
Painless package development for R
Devtools makes package development a breeze: it works with R’s existing conventions for code structure, adding efficient tools to support the cycle of package development. With devtools, developing a package becomes so easy that it will be your default layout whenever you’re writing a...Tags: Bioinformatics, R, Dev, Package, Devtools, RPackages, Tutorial
2934 days ago
Tags: Bioinformatics, Analysis, NGS, AccNET, Genome, Network
2777 days ago
Tags: Bioinformatics, Server, Cluster, Batch, SLURM, Tutorial
2933 days ago
Tags: Bioinformatics, Cutadapt, NGS, Reads, Fastq, Sequencing
2924 days ago
Tags: Bioinformatics, NGS, Assembly, de novo, Sequence, Assembler, Heterozygous
2924 days ago
Tags: Bioinformatics, NGS, Sequence, Andi, Evolution, Distance, Tool
2924 days ago
SATSUMA : Highly sensitive whole-genome synteny alignments.
Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does no...Tags: Bioinformatics, NGS, Sequence, Alignment, Synteny, Comparative genomics, Genomics
2924 days ago
PolyPhen-2: Prediction of functional effects of human nsSNPs
PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.Tags: Bioinformatics, PolyPhen-2, Prediction, Functional, Effects, nsSNPs
2914 days ago
Hagfish - assess an assembly through creative use of coverage plots
Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or identification of structural variation in a genome ...Tags: Bioinformatics, Hagfish, Assess, Assembly, Coverage, Plots, NGS, Structure, Variation, SV, Assembly, Genome
2916 days ago