RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently...Tags: Bioinformatics, NGS, Tk, Pipeline, Annotation, Tool, RASTtk
2914 days ago
GATB : Genome Analysis Toolbox with de-Bruijn graph
The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organis...Tags: Bioinformatics, NGS, Assembly, Tools, Tutorial, Toolbox
2913 days ago
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
2910 days ago
Tags: Bioinformatics, Analysis, NGS, AccNET, Genome, Network
2752 days ago
Tags: Bioinformatics, Cutadapt, NGS, Reads, Fastq, Sequencing
2899 days ago
Tags: Bioinformatics, NGS, Assembly, de novo, Sequence, Assembler, Heterozygous
2899 days ago
Tags: Bioinformatics, NGS, Sequence, Andi, Evolution, Distance, Tool
2899 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
2899 days ago
RCircos: an R package for Circos 2D track plots
RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate comple...Tags: Bioinformatics, NGS, R, Rcircos, Package, Plot, Circle, Genome, Genes, Visualization
2891 days ago
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roch...Tags: Bioinformatics, NGS, MOSAIK, Algorithm, Short-Read, Mapping, Genomics, Map, Tool
2891 days ago