There are many R software and bioconductor packages for NGS data analysis, some of them are as follows
Biostrings
The Biostrings package from Bioconductor provides an advanced environment for efficient sequence management and analysis in R. It...
Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.
Bioinformatics Textbook Track
Find more about Rosalind puzzle at...
ratt.sourceforge.net - RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.
It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between...
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...
wikis.utexas.edu - The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted...