What are the importante steps from getting the raw data from the sequencer until the assembly? I'm making voluntary work for a Teacher, they bought a new sequencer and gave me the introduction to find out what the .bam and .sam files are about. They told me to investigate bamtools and samtools for their filtering options, for example, sequence quality, base quality, trimming 5' and 3' ends, etc...
My actual question is, what should I do with the .bam and .sam files until I transform them to a FASTQ file. Actualy I found out that the filtering is much easyier utilizing fastx and fastq tools combined with the FastQC to verify the quality of the input/output.
The thing I'm looking for are the steps I have to take to make the raw data into something usable, like a genome assembly (which I gess is the last process in this work.) Regards and thanks in advance.
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Can you give us some more information? What sequencer is it? They vary quite a bit
The information ive got out of the FastQC is that it is a Iluminia or a Sanger sequencer. But i can give you a more precice answer after the weekend. Adicionaly I found out that by using the fasq_quality_filter I had to put the Q33 argument on the end identifiying that the input file had a Iluminina or Sanger input quality file.