Bioinformatics requires the use of complex programs written by computer scientists, which many biologists don't need to fully understand to effectively use these programs. These programs are referred to as "tools" since numerous tools are usually used to modify, align, and assemble genomes.
A scientist refers to the collective knowledge of calling programs, their toolbox, which allows them to work on the certain files with certain tools. This is analogous to any toolbox and the use of these tools is usually intuitive with the file name. For example, the use of SAM (Sequence Alignment/Map) Tools, will utilize files with the extension .SAM; however, it can also utilize a similar .BAM file as well. This tool is mainly used for evaluating and visualizing aligned reads and identifying any differences between the sample and reference genome available. A simple and more detailed work flow are shown below:
A scientist refers to the collective knowledge of calling programs, their toolbox, which allows them to work on the certain files with certain tools. This is analogous to any toolbox and the use of these tools is usually intuitive with the file name. For example, the use of SAM (Sequence Alignment/Map) Tools, will utilize files with the extension .SAM; however, it can also utilize a similar .BAM file as well. This tool is mainly used for evaluating and visualizing aligned reads and identifying any differences between the sample and reference genome available. A simple and more detailed work flow are shown below:
 |
| This is a broad overview of how SAMtools can be used in genomics and the goals of using this tool. Source:http://biobits.org/samtools_primer.html |
 |
| This work flow shows the use of numerous tools that gives a more detailed picture of what is happening. Furthermore, this workflow begins after step #2 of the above workflow and utilizes a reference genome to align the reads. Source:http://biobits.org/samtools_primer.html |
Comments
Post a Comment