BOL

Genome Information by Organism https://www.ncbi.nlm.nih.gov/genome/browse/#!/overview/ #Genome #information #NCBI

nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish...

#Polishing PacBio assemblies with Arrow and Pilon https://flowersoftheocean.wordpress.com/2018/04/16/polishing-pacbio-assemblies-with-arrow-and-pilon/ #polish #Pilon

#Database resources of the National Center for Biotechnology Information https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531099/ #NCBI

UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data,...

Biotechnology scientist jobs at http://www.dbtindia.nic.in/vacancies/ #Job #Biotechnology #DBTIndia #DBT

for i in $(ls *.ab1); do convert_trace -out_format scf < $i > ${i%.ab1*}.scf; done #Convert #AB12SCF #SCF #AB1

(smrttools) ➜ allBam for i in *.bam; do bamtools convert -format fasta -in $i -out $i.fasta; done #Convert #fasta

GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs....

We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline,...

A De Novo Genome #Assembly Algorithm for #Repeats and Nonrepeats https://www.hindawi.com/journals/bmri/2014/736473/

Biotechnology jobs in India http://www.dbtindia.nic.in/vacancies/

NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file...

Bioconda packages for bioinformatician https://conda-static.anaconda.org/bioconda/ #conda #bioconda #packages #list #tools

To decide which strategy should be our “preferred” genome assembly approach based on data rather than my gut-feeling about the “best assembly” I decided to do some testing with a known “true” reference E Coli K12 MG1655

Run a pipeline processing fast5s to a consensus in a single command. Recommended fixed "standard" and "fast" pipelines. Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath. Seemless...

Tutorial at http://sepsis-omics.github.io/tutorials/modules/roary/

Genomics, Proteomics & Bioinformatics https://www.journals.elsevier.com/genomics-proteomics-and-bioinformatics

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of...