I want to assemble and annotate the kiwi (bird) genome. What is the best genome assemble tool and genome annotation pipeline I can use?
We have 11 libraries with several insert sizes from Apteryx mantelli genomic DNA and sequenced 83 billion base pairs (Gb) from small insert-size libraries and 120 Gb from large-insert mate-pair Illumina libraries. The kiwi's genome size is about 1.6 Gb. The assembled contigs and scaffolds cover approximately 96% of the complete genome with an average sequence coverage of 35.85-fold after correction.
The ones I have found from my research are MaSuRCA, Platanus, ALLPATHS-LG and ABySS for the genome assembly and BRAKER2, MAKER and CAT pipelines for genome annotation. For the de novo gene prediction and annotation we can also provide 47.5 Gb of transcript sequence data from kiwi embryonic tissue together with the de novo gene predictions and protein evidence from three well-annotated bird species.
Thank you in advance.
My goal is to re-assemble and re-annotate the genome of kiwi from the sequencing data provided by this article: DOI 10.1186/s13059-015-0711-4 I want to use new tools and pipelines in order to increase the efficiency of the assembly and the annotation.