I did a transcriptome assembly of Illumina SE and PE reads using Trinity, but the N50 values for my assembly are very low. Here is the summary:
Total trinity 'genes': 748144 Total trinity transcripts: 916206 Percent GC: 43.83 Contig N10: 1765 Contig N20: 1064 Contig N30: 677 Contig N40: 477 Contig N50: 369 Median contig length: 253 Average contig: 364.39 Total assembled bases: 333854406
In addition to Illumina PE and SE data, I also have PacBio full-length transcripts data. Is there any way I can perform a hybrid transcriptome assembly? Need your ideas on it.
PBcR with Celera assembler seems to be one option that corrects PacBio reads and performs hybrid assembly, but 1) it seems to be significantly slow as mentioned by authors, 2) it is not clear from its documentation whether it will use Illumina reads beyond the reads correction step i.e. for final assembly and 3) no example provided by authors on how to use it for 'transcriptome' hybrid assembly. These issues with PBcR makes me think that it is a slow error correction tool which uses only the PacBio reads for final assembly. Are there any other options for de novo hybrid assembly of transcriptome?