bruvellu / acoelomorpha

Effort to solve the position of acoels in the animal tree of life.

Phylogenomics of Acoelomorpha

Objective: solve the phylogenetic position of acoels and nemertodermatids. Read more.

Progress:

• Developed a script/module to search and filter SRA records.
• Searched and got a list of SRA packages.
• Tested workflow with a few organisms.
• Defined curation criteria: if unique, yes; if multiple, pick mixed tissues; if tissue specific, merge multiple until 40M reads.
• Running assemblies.

Plan:

• Continue building assemblies.
• Solve issues like quality offset, no rRNA, too large samples, multiple samples.
• Define list of additional RNAseq assemblies.
• Define list of additional genomic assemblies.
• Study phylogenetics.

acoelomorpha's Issues

Automatic update of package status

I was assigning status to each package manually (downloading, assembling, failed, assembled, phred64, norrna, and discarded) on a spreadsheet. With a thousand packages this does not scale, so it makes sense to keep a central CSV file which gets updated programatically: sra/sra.csv.

I wrote a module to perform this and it currently merges packages from different queries. It lacks a way to update the status column of a package. Make it work on the command line also?