Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny
Catchen, Julian; Amores, Angel; Bassham, Susan (2020), Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny, Dryad, Dataset, https://doi.org/10.5061/dryad.gtht76hjm
This dataset consists of several genome integrations, combining an assembled genome and a genetic map, to create chromosome-level assembly. The software chromonomer is used for the integration. There are three integrations of teleost fish, including:
- Gulf pipefish (Sygnathus scovelli)
- Platyfish (Xiphophorus maculatus)
- Black rockcod (Notothenia coriiceps)
The gulf pipefish integration began with data from the sequence read archive (SRA), NCBI BioProject Accession PRJNA355893, while the Sygnathus acus reference genome (NCBI accession GCA_901709675.1, BioProject PRJEB32741) was used as a base for the Sygnathus scovelli gene annotationa. The platyfish integration began with SRA data from NCBI accession GCA_002775205.2, BioProject PRJNA72525, with raw read data obtained from SRA accessions SRR7207855 - SRR7207868. The black rockcod genome assembly was obtained from NCBI accession GCA_000735185.1, BioProject PRJNA66471.
The genetic map for each fish is included in this repository, named *_unprocessed_consensus_genetic_map.tsv and the RADseq markers corresponding with the map are also provided as all_markers.fa.gz in each respective directory.
Each integration includes a shell script (chrr.sh) outlining how the chromonomer software was executed.
National Science Foundation, Award: 1645087
National Science Foundation*, Award: 1543383
National Institutes of Health, Award: R01 ODO11116
National Institutes of Health, Award: R24 RR032670
National Science Foundation, Award: 1543383