A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
Thanks for this great tool! However, I have a few questions on input for cobra
Now I'm using megahit to assembly (I just know from #3 that it may generate many chimeric contigs, but spades may run out of memory when assembly environmental samples). In megahit intermediate results, it will provide a file named ./intermediate_contigs/k141.contigs.fa, in which there are many small contigs < 200 bp (which will be filtered in ./final.contigs.fa). My question is, which contig file is more recommended to be used as --fasta FASTA input?
Is it possible to just use the final.contigs.fa as --query QUERY file, or a filtered version with all contigs longer than given length (i.e. 1000 or 2500 bp)? In another words, can cobra be used before virus contigs annotation and MAG binning?
Thanks for this great tool! However, I have a few questions on input for cobra
./intermediate_contigs/k141.contigs.fa, in which there are many small contigs < 200 bp (which will be filtered in./final.contigs.fa). My question is, which contig file is more recommended to be used as--fasta FASTAinput?final.contigs.faas--query QUERYfile, or a filtered version with all contigs longer than given length (i.e. 1000 or 2500 bp)? In another words, can cobra be used before virus contigs annotation and MAG binning?Regards, hwrn