Closed vsiverson closed 11 years ago
The velvet assembly should use a k-mer of 19 not 15, because 15 produces a horrible assembly.
Use this command instead of the one listed in the User Guide:
velveth_de lambda_asm/ 19 -fastq.gz -shortPaired lambda_trim.mates.fastq.gz -short lambda_trim.single.fastq.gz > lambda_asm.velveth_de.log 2>&1 velvetg_de lambda_asm/ -scaffolding no -read_trkg no -ins_length auto -ins_length_sd auto -exp_cov 50 -cov_cutoff 5 -min_contig_lgth 50 > lambda_asm.velvetg_de.log 2>&1
Fixed in version 0.4.3
The velvet assembly should use a k-mer of 19 not 15, because 15 produces a horrible assembly.
Use this command instead of the one listed in the User Guide: