Ka Ming Nip
Ka Ming Nip
Yes, please include the short reads, which should improve the error correction step. Your command looks correct. You can include multiple read file paths separated by the whitespace character, e.g....
Was there any ribosomal RNA depletion before sequencing? It is possible that your read set is predominantly rRNA. You could check the assembled transcripts for rRNA. The lower number of...
> No rRNA depletion was carried out. Do you have an advice how I can check of the presence of the rRNA in the assembly? You can try SILVA's web...
The input k-mers are hashed with ntHash. So, they should be nucleotide sequences, which are strings of A, C, G, T, and U.
Hello @mtmcgowan , That is roughly 3.4 billion reads in total (99 * 35 million), which is probably too many for 250 GB RAM. So, I suggest that you assemble...
Hi @mtmcgowan With Trans-ABySS version 2, you don't need many small increments in k. For each accession (i.e. 3 replicates combined), you can probably just use 3 k-mer sizes (e.g....
You can use as many/little k-mer sizes as you want.
@kokyriakidis Since you are using a small k-mer size (ie. 32), I would recommend recompiling ABySS with a smaller max kmer size. The default is 128, which is 4 times...
If you assemble at k=40 on different machines: - the peak memory usage would be the same - the set of assembled sequences should be the same However, the merged...
@kokyriakidis Trans-ABySS does not use the Bloom filter de bruijn graph. So, running ntCard would not help with your memory issue at all. Please recompile ABySS with a smaller max...