5.1 years ago by
I can try to answer the question now, note that I have probably as some tools are dependent on others.
Velvet (probably Oases too) - Replace N's with A
Abyss (probably Trans-Abyss too) - Replace N's based on consensus sequences that fill that base, consensus sequence of 90% identity through DIALIGN-TX aligner
SOAPdenovo2, SOAPdenovo-Trans - Replace N's with G
ALLPATHS - Ambiguous bases are saved as random bases
Rnnotator - Uses velvet, so probably N's to A
IDBA - From the authors it is understood that sequencing depth is considered for assembly,
Basically, we try to correct the graph based on the sequencing depth. It identifies similar paths and removes paths with very low sequencing depth comparing to neighbors. Note that it doesn't introduce new k-mers in this process. The assumption is that the actual sequence must appear in the graph and have higher depth.
Minia - If there are ambiguous bases in the input, i.e. N's in reads, then Minia cut reads around them: precisely, it discards any k-mer containing at least one N.
Trinity - Ignored first, later treated as mismatches
Non-[GATC] characters will be ignored during the early phases of Trinity (jellyfish, inchworm, and chrysalis- I think), and then likely treated as mismatches during the final butterfly phase. Trinity simply isn't compatible for the most part, though shouldn't error-out as a result of such chars.
CLCbio - I do not have a commercial license so I do not receive support, in this case those with a commercial license should try asking them as their code is unreadble
modified 5.1 years ago
5.1 years ago by
Rohit • 1.4k