GS De novo assembler

Summary

Performs assembly of reads and generates contigs. Current Version 2.5.3. Full Roche manual.

Input options

• Sff files
• Fasta files
• Converted Sanger data- Fasta files and corresponding Quality files

Output options

• Consensus sequence (contigs)
• Corresponding quality scores
• ACE files
• Assembly metrics files
• Pairwise alignments
• Read status file
• Alignment views - GUI only
• Flowgrams - GUI only
• For paired end data, scaffold files

Running GS De Novo assembler

GUI Assembler - 

• Can be accessed by typing gsAssembler
  

Commandline Assembler - 

• runAssembly -o /data/filename /data/R_/D_
• For paired end data, runAssembly -o /data/filename -p /data/R_/D_
  

Some options

• Incremental de novo assembly - will allow you to add more data to the assembly when needed.
• Large or complex genomes - for genomes larger than 15 Mb, use this option.
• Trimming database file - Provide a file with fasta sequences that need to be removed (trimmed) from reads (like vectors).
• Screening database file - Provide a file containing contamination sequences for screening.
• cDNA assembly- use option -cdna
  

Things to remember

• Reads shorter than 50 bp long are removed by default. 
• The tool is more powerful and produces better assemblies when using sff files than just fasta files as input. The flowgrams are used when computing signals.
• It is a good idea to use Repeatmasker to handle repeats before assembly.
• The current assembler version uses 3 to 4 bytes of memory per base and is equipped to run only on a single processor. In cases where memory is not enough to do an assembly, try the incremental de novo assembly option.