Low sum in ragoo.fasta

Hello,

I am attempting to run Ragoo using a long-read assembly as the ‘reference’. After running Ragoo with the following command:

ragoo.py -t 4 -b -C ${assembly} ${ref}

My output ragoo.fasta file seems to be missing a lot of bases. The original assembly is ~2.7Gb, but the output fasta file has ~736 Mb only.

Any idea about what is happening to the outstanding sequences, or is this expected behaviour? The chimera.broken.fa file is the correct size, so it seems that things are being lost after that stage somewhere.

Thanks! Lauren

[malonge]

Hi there,

After testing the code with your data, I believe I understand the problem.

When -C is invoked, a single file for each of the unplaced contigs is written in the intermediate output directory. Since your contigs had roughly 1M unplaced contigs, I assume this became a problem for your file system, thus leading to the truncated ragoo.fasta file.

Indeed, if one does not use -C, ragoo.fasta contains the expected amount of sequence.

In future versions of RaGOO, the intermediate output will be restricted to exactly 2 files regardless of the -C option. I believe that should solve the “low sum” problem.

Additionally, it is true that RaGOO was not designed for more fragmented assemblies of larger genomes. To address this, future versions of ragoo will allow the user to lower the minimum alignment length, thus allowing for more contigs to be placed.

I will test out your data again when these features are implemented.

Thanks

[lcoombe]

My ‘reference’ is another human assembly using a different assembler. The original ragoo.fasta file has ~727 Mbp in it, vs ~2.4 Gbp in the file with manually concatenating sequence.