Even with a correct reference sequence, some regions were still not assembled properly (e.g., accD, ycf1) and some assembly mistakes from the original assembly were recreated (e.g., an erroneous 5 bp deletion in the middle of rbcL causing a frameshift).
Steve Rogers, general manager of the Middletown factory, said they were struggling early in the year with assembly mistakes and safety issues.
This finding may be partially attributed to sequence assembly mistakes during Illumina sequencing.
These duplications were not detected by FISH, suggesting that the duplications could be assembly mistakes.
Apparently, due to the assembly mistakes in the zebrafish genome, some of the syntenic breaks may be due to the still poor assembly of the zebrafish genome.
The unigenes without hits probably belonged to untranslated regions, noncoding RNA, short sequences not containing a protein domain or assembly mistakes.
When using two different insert size libraries, coverage improves but relocation and redundancy scores are reduced, indicating more assembly mistakes with the 3Kpb + 8Kbp paired read mixture.
Such assembly mistakes will be probably avoided if using longer reads (since repeats longer than the read length pose problem during assembly) or, alternatively, can be resolved a posteriori using GRAAL.
In other cases it was noticed that a reported ORF might be shorter than homologous ORFs due to stop codons likely created by sequencing or assembly mistakes (Additional file 7).
The annotations of protein coding regions, ribosomal DNA (rDNA), and sequences corresponding to transfer RNAs (tRNAs) were improved by fixing annotation and assembly mistakes (e.g., no start or stop codon, internal stop codons, frameshifts, endpoints of tRNA sequences) through examination of the actual assembly of the short reads at that location in Tablet vers.
Seven of the 29 validated sequences were identical to the sequences obtained from Illumina sequencing, whereas 18 of which had less than 10 mismatched nucleotides and 4 of which had more than 10 mismatched nucleotides, which might be partially attributed to sequence assembly mistakes during the Illumina sequencing.
