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armbrustlab / SEAStAR

SEAStAR is a package of tools supporting the construction of complete analysis pipelines for next-generation (Illumina®, SOLiD™) sequencing data generated from environmental samples.
https://armbrustlab.ocean.washington.edu/tools/seastar/
GNU General Public License v3.0
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Bad k-mer value for Velvet assembly in Quick Start section of User Guide #3

Closed vsiverson closed 11 years ago

vsiverson commented 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
vsiverson commented 11 years ago

Fixed in version 0.4.3