Galaxy |

Canu assembler (version 2.2+galaxy0)

Input reads:

Haplotypes for Trio Binning Assemblies

Haplotypes for Trio Binning Assembly 0

Technology:

Processing:

To restrict canu to only a specific stage, use:

Estimated genome size (e.g. 8.0m, 15k, 2g):

Maximum raw overlap mismatch:

The defaults are 0.300 for PacBio reads and 0.500 for Nanopore reads.

Maximum corrected overlap mismatch:

The allowed difference in an overlap between two corrected reads. Assemblies of low coverage or data with biological differences will benefit from a slight increase in this. Defaults are 0.045 for PacBio reads and 0.144 for Nanopore reads.

Minimum read length:

Minimum overlap:

Minimum Input Coverage:

Target coverage for corrected reads:

Additonal options:

Additional specifications provided in a canu spec file.

Stop the assembly if read coverage is too low to be useful:

Coverage is checked whene when input sequences are initially loaded into the sequence store, when corrected reads are generated, and when read ends are trimmed off.

Contig Filters

Contig Filters 0

Canu specializes in assembling PacBio or Oxford Nanopore sequences. Canu operates in three phases: correction, trimming and assembly. The correction phase will improve the accuracy of bases in reads. The trimming phase will trim reads to the portion that appears to be high-quality sequence, removing suspicious regions such as remaining SMRTbell adapter. The assembly phase will order the reads into contigs, generate consensus sequences and create graphs of alternate paths.

For eukaryotic genomes, coverage more than 20x is enough to outperform current hybrid methods, however, between 30x and 60x coverage is the recommended minimum. More coverage will let Canu use longer reads for assembly, which will result in better assemblies.

http://canu.readthedocs.io