2233 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It...mounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1...million single-end reads onto the human reference genome....2233 days ago
mScaffolder: A comparative genome scaffolding tool
A comparative genome scaffolding tool based on MUMmer mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer...and then orders and orients the contigs of the candidate genome...2210 days ago
SWALO: Scaffolding with assembly likelihood optimization
SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to atif.bd@gmail.com.2205 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome...2205 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence anno...linked maps can be explored using any web browser, allowing rapid genome...2205 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optio...ne Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes...2196 days ago
2192 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq...reads to be aligned against the reference genome and significantly improves ou...cies (e.g., Hyacinth macaw); Reference genome-...2192 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist:...2041 days ago