BOL

platanus.bio.titech.ac.jp - Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. The latest version is 1.2.4. To cite Platanus, please use the...

cutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an...

www.sanger.ac.uk - PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference. IMAGE, an...

github.com - Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cshlp.org/content/27/5/747.full An ipython notebook to...

arthropods.eugenes.org - EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University,...

New SPAdes 3.15.0.0. announced by the SPADes team

metagraph.ethz.ch - The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle,...

https://pandoc.org/ - If you need to convert files from one markup format into another, pandoc is your swiss-army knife. Pandoc can convert almost all formats https://pandoc.org/index.html

edwards.sdsu.edu - if you have less time, then use three ways mentioned in bookmark link to extract/download all fasta sequences in single click given that you already have a list of GIs or accession IDs . Alternatively, use one liner perl script: perl -ne...

Sequencing of hundreds of newborns