BOL

User-friendly tools for the normalization and visualization of deep-sequencing data

cran.r-project.org - Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in...

http://genomeribbon.com/ - Visualization has played an extremely important role in the current genomic revolution to inspect and understand variants, expression patterns, evolutionary changes, and a number of other relationships. However, most of the information in...

www.vicbioinformatics.com - Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files...

https://dfast.nig.ac.jp/ - We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its...

http://assemblytics.com/ - Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip...

sepsis-omics.github.io - This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and...

github.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...

ftp.ncbi.nih.gov - Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ... ftp://ftp.ncbi.nih.gov/genomes/ https://hgdownload.soe.ucsc.edu/downloads.html

github.com - odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. Careful encoding of graph entities allows odgi to efficiently...