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Anyone have any experience using Abyss to assembly Ion Torrent data? I am getting some pretty awful results I think.
I have 100X MiSeq coverage (2x150) and 100X Ion Torrent data (avg read length a little under 200). I did a kmer parameter sweep on both. My best MiSeq assemblies are getting me right around 200contigs, which is pretty awesome. Unfortunately Ion Torrent is up around 10,000.
I think it is likely I am doing something wrong, but not sure what.
MiSeq command structure:
abyss-pe -j 8 k=43 name=k43 in='MiSeq_100X_1.clipped.fastq.gz MiSeq_100X_2.clipped.fastq.gz' > k43.log 2>&1
Ion structure:
abyss-pe -j 8 k=43 name=k43 se='Ion_PGM3_100X.clipped.fastq.gz' > k43.log 2>&1
I'm going to be trying out some other assemblers, but just wondering what the f is going on here...
I have 100X MiSeq coverage (2x150) and 100X Ion Torrent data (avg read length a little under 200). I did a kmer parameter sweep on both. My best MiSeq assemblies are getting me right around 200contigs, which is pretty awesome. Unfortunately Ion Torrent is up around 10,000.
I think it is likely I am doing something wrong, but not sure what.
MiSeq command structure:
abyss-pe -j 8 k=43 name=k43 in='MiSeq_100X_1.clipped.fastq.gz MiSeq_100X_2.clipped.fastq.gz' > k43.log 2>&1
Ion structure:
abyss-pe -j 8 k=43 name=k43 se='Ion_PGM3_100X.clipped.fastq.gz' > k43.log 2>&1
I'm going to be trying out some other assemblers, but just wondering what the f is going on here...