We would like to complete our description of SOAPdenovo2 commands and get into more interesting topics, such as how good the quality of the assembly is. Before we get there, here are the last two steps of assembly -
‘map’
./SOAPdenovo-63mer-v2.04.3 map -s config_file -g outPG -p 32
The above command maps the reads back on to the assembled contigs. The command needs at least two parameters – name of the configuration file and prefix for the graph. In addition, we gave it the number of processors (‘-p 32′) to speed up the run. All parameters were explained in our previous commentaries here and here.
The map command took several hours to run, and produced four output files.
outPG.readInGap.gz – very large file containing information about the reads that mapped in the gaps between contigs.
outPG.readOnContig.gz – very large file containing information about the reads that mapped onto gap.
outPG.newContigIndex – a text file containing some kind of index.
outPG.peGrads – a tiny file with some kind of statistical information on the mate pair sizes.
‘scaff’
./SOAPdenovo-63mer-v2.04.3 scaff -g outPG -p 32
The above command completed the assembly by utilizing longer mate pair reads and joining contigs into scaffolds. The process of building up of contigs (‘SOAPdenovo contig’) did not use mate pairs, because we did not give that option in our config file.
This step took about an hour and produced a number of output files. At this point, we cared about one and only one file, and its name is shown at the bottom.
outPG.asm, outPG.bubbleInScaff,outPG.contig4asm, outPG.contigPosInscaff
outPG.gapSeq, outPG.links,outPG.scaf_gap, outPG.scafSeq, outPG.scafStatistics
outPG.scaf – The final assembly.