Plasmodium Laverania

Comparing to genome assembly of all other six Plasmodium species within the subgenus Laverania(Otto et al. 2018)

Theoretical timeline of the P. Laverania subgenus

tree of rRNA of all of P. laverania
Code
genomes = readr::read_tsv("assembly_study_links.txt")
create_dt(genomes)

/tank/data/plasmodium/genomes/pLaverania/genomes/PadleriG01.fasta
/tank/data/plasmodium/genomes/pLaverania/genomes/PbillcollinsiG01.fasta
/tank/data/plasmodium/genomes/pLaverania/genomes/PblacklockiG01.fasta
/tank/data/plasmodium/genomes/pLaverania/genomes/PgaboniG01.fasta
/tank/data/plasmodium/genomes/pLaverania/genomes/PpraefalciparumG01.fasta
/tank/data/plasmodium/genomes/pLaverania/genomes/PreichenowiG01.fasta

tandem repeat finder

Code
/bin/ls /tank/data/plasmodium/genomes/pLaverania/genomes/*.fasta | sed 's/.*\//g'  | sed 's/.fasta/g' > species.txt

runTRFCmds.txt

Code
CMD:elucidator runTRF --fasta /tank/data/plasmodium/genomes/pLaverania/genomes/{SPECIES}.fasta --supplement --dout trf_{SPECIES} --overWriteDir
{SPECIES}:species.txt
Code
nohup elucidator runMultipleCommands --cmdFile runTRFCmds.txt --numThreads 6 &

nucmer

runNucmerCmds.txt

Code
CMD:nucmer /tank/data/genomes/plasmodium/genomes/pf/genomes/Pf3D7.fasta /tank/data/genomes/plasmodium/genomes/pLaverania/genomes/{SPECIES}.fasta --prefix {SPECIES}_to_Pf3D7_nucmer > nuclog_{SPECIES}.txt 2>&1 && show-coords -T -l  -c -H {SPECIES}_to_Pf3D7_nucmer.delta | elucidator parseNucmerResultsToBed  --coordsOutput STDIN --overWrite --out {SPECIES}_to_Pf3D7_nucmer.delta.bed  && elucidator splitColumnContainingMeta --file {SPECIES}_to_Pf3D7_nucmer.delta.bed --delim tab --column col.6 --removeEmptyColumn  --addHeader  --overWrite --out {SPECIES}_to_Pf3D7_nucmer.delta.tsv && elucidator filterBedRecordsByLength --bed {SPECIES}_to_Pf3D7_nucmer.delta.bed --minLen 2000 --overWrite --out minlen2000_{SPECIES}_to_Pf3D7_nucmer.delta.bed && elucidator bedGetIntersectingGenesInGff --gff /tank/data/genomes/plasmodium/genomes/pf/info/gff/Pf3D7.gff --extraAttributes description --bed minlen2000_{SPECIES}_to_Pf3D7_nucmer.delta.bed --out minlen2000_{SPECIES}_to_Pf3D7_nucmer.delta_withGeneInfo.bed
{SPECIES}:species.txt
Code
nohup elucidator runMultipleCommands --cmdFile runNucmerCmds.txt --numThreads 6 &

References

Otto, Thomas D, Aude Gilabert, Thomas Crellen, Ulrike Böhme, Céline Arnathau, Mandy Sanders, Samuel O Oyola, et al. 2018. “Genomes of All Known Members of a Plasmodium Subgenus Reveal Paths to Virulent Human Malaria.” Nat Microbiol 3 (6): 687–97.