BOL

Cells accept bioinformatics papers https://www.mdpi.com/journal/cells/special_issues/bioinformatics_cells

quantumzyme in india http://quantumzyme.com/

QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size). QUAST-LG is included in the QUAST  package starting from version 5.0.0 (download the latest release). Run QUAST as...

Is It #Ordered Correctly? #Validating #Genome #Assemblies by Optical Mapping http://www.plantcell.org/content/30/1/7

Genome assembly tutorial https://astrobiomike.github.io/genomics/de_novo_assembly

Nucleus journal accept bioinformatics tool and software papers https://www.springer.com/life+sciences/cell+biology/journal/13237

MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite...

Gene prediction tools http://genome.crg.es/courses/laCaixa05/Prediction/index.html #Genes #Predicts

Export the PATH in Linux $ PATH="/home/urbe/Tools/ALLHiC/scripts:${PATH}" and then $ export PATH #Path #Set #Variable

Add number in fasta header $ awk '/^>/{$0=$0"_"(++i)}1' infile.fa #fasta #header #add #number #count

The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed...

Blast database https://ftp.ncbi.nih.gov/blast/db/ #blast #database

FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et...

#Split the #BAM file $ /home/urbe/Tools/bamtools/bin/bamtools split -in improved3.fasta.sorted.bam -reference #bamtools

Extract sequence by ids $ xargs samtools faidx Adineta_vaga.v2.pep.fa < AlienIds > allAlienSeq.fa #Extract #Ids #Sequences

The package is open source and freely available at GitHub (https://github.com/biotite-dev/biotite). This package is simple to use especially for the beginners in programming and computationally efficient because of the implementation of Numpy and...

The BETSY provides a command-line interface and available at https://github.com/jefftc/changlab. A user first searches in the knowledge base for desired output and then BETSY develops an initial workflow to produce that data which is later...

https://iisc.ac.in/post-docs/ IISc PostDoc #postdoc #iisc

Bioinformatics training http://ce3c.ciencias.ulisboa.pt/training/?cat=13 #Training