What’s the Answer: Open Thread (NGS Tools)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the
community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

Question of the week:

Now we are analysing NGS data, and I wonder if you know some collections of bioinformatics tools which can help me (like biopieces).

There were a few good answers with a good suggestion of lists of tools for analysis and preparation of Next-Generation Sequencing tools. Here’s one answer, click the link above for the rest:

(after some advice about mastering scripting language and unix commands…)

  1. learn the most used bioinformatics tools. e.g.:
    • one (or preferably many) short-read aligners
    • samtools
    • an NGS viewer (IGV is a good one to start)
    • Bedtools
    • A means to view and filter your NGS reads
    • and certainly many others depending on your specific focus.
  2. Then start to learn some of the common data repositories. e.g.: