BOL

PacBio data to download http://www.cbcb.umd.edu/software/PBcR/original/index.html #pacbio #data

Diploid Assembly of a Puerto Rican Female Adds a Rich Resource to Population-Specific Reference Genomes

https://www.ebi.ac.uk/about/news/announcements/25-genomes-UK-species #Genomes #Sequenced #UK

https://pb-falcon.readthedocs.io/en/latest/quick_start.html#quick-start #Falcon-Unzip #Genome #Assembly

https://blog.rstudio.com/2018/10/05/r2d3-r-interface-to-d3-visualizations/ #r2d3 #visualization

GO::TermFinder http://gmod.org/wiki/GO::TermFinder

Long reads base bacterial genome assembly https://inf-biox121.readthedocs.io/en/2016/Assembly/practicals/07_Assembly_using_minasm+racon.html

Nanofilt steps https://gigabaseorgigabyte.wordpress.com/2017/06/05/trimming-and-filtering-oxford-nanopore-sequencing-reads/

Understanding Megan http://ab.inf.uni-tuebingen.de/data/software/megan6/download/MeganTutorialApril2018.pdf

Bacterial genome assembly tutorial http://evomics.org/learning/assembly-and-alignment/2017-assembly-lab/

Long reads assembly PPT https://www.msi.umn.edu/sites/default/files/Badalamenti_PacBio_tutorial_12-10-2014.pdf

Long reads assembler https://zenodo.org/record/345098/files/scientific_reports_assembly_long_reads%282%29.pdf

RapClust is a tool for clustering contigs from de novo transcriptome assemblies. RapClust is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. Specifically,...

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...

This is a tool for detecting structural variations using soft-clipping information From SAM files. https://github.com/shinout/clipcrop

VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store...

Mapping subreads https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf #R

nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where...

GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via...