Scripts and intermediate results for de novo assembly, annotation and analysis of genomes

Here we are sharing the scripts and intermediate results we generated in our genomics studies on a couple of Lepidoptera species. We will keep updating our website as soon as new results are available.
Please be aware that the scripts we shared here are the working scripts that we used in our own study. You usually need to modify the paremeters accordingly so that they may work in your case.
If you are interested in some of our results/scripts but are having trouble using them, Please contact Qian Cong at congqian1986@gmail.com

Our in-house Python scripts

Scripts to merge equivalent segments from homologous chromosomes after intial assembly here.
Scripts to predict repeats based on coverage of the genome by sequence reads here.
Scripts to select good gene models for gene predictor training here.
Scripts to calculate synteny here.

Our genome assemblies and annotations (most recent)

Official genome assembly for Papilio glaucus v1.1 can be downloaded here.
Official gene annotation for Papilio glaucus v1.1 can be downloaded here.
Official genome assembly for Lerema accius v1.1 can be downloaded here.
Official gene annotation for Lerema accius v1.1 can be downloaded here.
Official genome assembly for Phoebis sennae v1.1 can be downloaded here.
Official gene annotation for Phoebis sennae v1.1 can be downloaded here.
Official genome assembly for Calycopis cecrops v1.1 can be downloaded here.
Official gene annotation for Calycopis cecrops v1.1 can be downloaded here.
Official genome assembly for Pieris rapae v2 can be downloaded here.
Official gene annotation for Pieris rapae v2 can be downloaded here.

Other intermediate results

Intermediate results for the Papilio glaucus genome project
Intermediate results for the Lerema accius genome project
Intermediate results for the Phoebis sennae genome project
Intermediate results for the Calycopis cecrops genome project
Intermediate results for the Pieris rapae genome project

Please cite:

Tiger Swallowtail Genome Reveals Mechanisms for Speciation and Caterpillar Chemical Defense. (2015). Cong Q, Borek D, Otwinowski Z, Grishin NV. Cell Rep. doi: 10.1016/j.celrep.2015.01.026. [PMID: 25683714]

Skipper genome sheds light on unique phenotypic traits and phylogeny. (2015). Cong Q, Borek D, Otwinowski Z, Grishin NV. BMC Genomics. 16:639. doi: 10.1186/s12864-015-1846-0. [PMID: 26311350]

Speciation in Cloudless Sulphurs gleaned from complete genomes. (2016). Cong Q, Shen J, Warren AD, Borek D, Otwinowski Z, and Grishin NV. Genome Biology and Evolution. doi:10.1093/gbe/evw045. [PMID: 26951782]

Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence. (2016) Cong Q, Shen J, Borek D, Robbins RK, Otwinowski Z, and Grishin NV. Sci Rep. 6:24863. doi: 10.1038/srep24863. [PMID: 27120974]

Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins. (2016) Shen J, Cong Q, Kinch LN, Borek D, Otwinowski Z, Grishin NV. F1000Res. 5:2631. doi: 10.12688/f1000research.9765.1. [PMID: 28163896]