seq.crg.es - The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using short-read deep sequencing data. In its present implementation MIRO is especially adapted for the analysis of...
http://shinyheatmap.com/ - Background: Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets. Visualizing such big data has posed technical challenges in biology, both in...
github.com - LINKS is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads,...
http://last.cbrc.jp/ - LAST can:
Handle big sequence data, e.g:
Compare two vertebrate genomes
Align billions of DNA reads to a genome
Indicate the reliability of each aligned column.
Use sequence quality data properly.
Compare DNA...
it.informatik.uni-tuebingen.de - The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions,...
www.australianprostatecentre.org - Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom...
www.baseclear.com - SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or...
Following are the list of journals publishing pint-sized articles go by various names, such as genome reports, genome announcements, genome notes or genome letters, but will be referred to here broadly as genome reports.
www.nature.com - GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve...
github.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch.
To use the latest version,...