Part of the reason R has become so popular is the vast array of packages available at the cran and bioconductor repositories. In the last few years, the number of packages has grown exponentially!
This is a short post giving steps on how to...
en.wikibooks.org - Employing different technologies, the purpose of NGS platform is to decode the identity or modification on the nucleotides. NGS platforms evolve quickly and capture the main stream.
This bookmark is created to provide NGS online books links.
The goal of our research is to better understand the biology of microbial organisms of significant ecological, veterinary and medical importance.
To achieve this goal, our team combines the power of next generation DNA sequencing and...
National Institute of Plant Genome Research, New Delhi is an Autonomous Research Institution funded by Department of Biotechnology, Ministry of Science & Technology, Govt. of India, to pursue research on various aspects of plant genomics. The...
microscope.readthedocs.org - Microscope Platform user documentation.
The MicroScope platform is available at this URL:
https://www.genoscope.cns.fr/agc/microscope
github.com - Pilon is a software tool which can be used to:
Automatically improve draft assemblies
Find variation among strains, including large event detection
Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads...
broadinstitute.github.io - Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF...
mira-assembler.sourceforge.net - MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assembles/maps reads gained by
electrophoresis sequencing (aka Sanger sequencing)
454 pyro-sequencing (GS20, FLX or Titanium)
Ion...
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.
Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the...