Genome sequences of some genomes, specially the Refseq genomes (starts with GCF_), are stored in muliple multiple-fasta files as shown below:
./GCA_021436885.1/ncbi_dataset/data/GCA_021436885.1/chr1.fna
./GCA_021436885.1/ncbi_dataset/data/GCA_021436885.1/chr2.fna
./GCA_021436885.1/ncbi_dataset/data/GCA_021436885.1/chr3.fna
./GCA_021436885.1/ncbi_dataset/data/GCA_021436885.1/chr4.fna
./GCA_021436885.1/ncbi_dataset/data/GCA_021436885.1/unplaced.fna
Fragmented storage brings inconvenience to subsequent analysis. Therefore, I wrote this script to merge these fragmented genome sequences into one FASTA file.
Input is a tab-delimited file as shown below:
GCA_021398005.1 ./GCA_021398005.1/ncbi_dataset/data/GCA_021398005.1/GCA_021398005.fna
GCA_021436885.1 ./GCA_021436885.1/ncbi_dataset/data/GCA_021436885.1/chr1.fna
Output is a FASTA file.
output_directory/GCA_021398005.1.fna
Recommended usage
find . -name '*.fna' | grep -v -e 'cds' -e 'rna' -e 'protein' | awk -F '/' '{print $2"\t"$0}' | merge_assembly_pieces.py - -o output_directory
When we are carrying out a big project including thousands of genomes, we should summarize all BUSCO results and further to remove bad assemblies.
For this purpose, I wrote summary_BUSCO_results.py.
Recommended usage
find . -name 'short_summary.specific*txt' | summary_BUSCO_results.py - | sed 's/genome_label/Assembly/;s/.fna//' > busco_statistics.tsv
Results as shown below:
Assembly C S D F M Complete BUSCOS (C) Complete and single-copy BUSCOs (S) Complete and duplicated BUSCOs (D) Fragemented BUSCOs (F) Missing BUSCOs (M) Total BUSCO groups searched
GCA_013390195.1 97.8% 97.5% 0.3% 0.2% 2.0% 1669 1664 5 3 34 1706
GCA_003568745.1 97.0% 96.3% 0.7% 0.8% 2.2% 1655 1643 12 13 38 1706
GCA_014705165.1 97.6% 97.1% 0.5% 0.4% 2.0% 1665 1656 9 6 35 1706