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4. GS De Novo Assembler and GS Reference Mapper Appendices : 4.13 Assembling with FASTA Reads Obtained Using the Sanger Sequencing Method
4.13
Assembling with FASTA Reads Obtained Using the Sanger Sequencing Method
4.13.1 Simple Sanger Reads
4.13.2 Sanger Reads with available Quality Scores
4.13.3 Sanger Read Annotations
4.13.4 Recommended Method for Including Sanger Reads
Introducing reads obtained using the Sanger sequencing method (Sanger reads) into an assembly or mapping can be more complicated than including 454 Sequencing reads, because Paired End information, trimming information and vector (and other non-sample) information is often not directly associated with the read sequences. To utilize the full capabilities of the GS De Novo Assembler or the GS Reference Mapper, the FASTA files of input Sanger reads must be prepared so that they provide the software with the Paired End, trimming and non-sample information (see the Overview for a description of FASTQ files, which can simplify this process). This section describes how the data analysis software applications may use Sanger read data FASTA files.