Velvet is a de novo assembler intended for next generation reads. Velvet is ideal for assembling Illumina sequencing reads of bacterial genomes on a mid range Mac. With paired read data it produces very good contigs. For example a 7Mb genome with an N50 of 103kbp was produced from 16 million paired Illumina reads in one hour on a 16GB 2007 Mac Pro.
Note that you can hold down the <shift> key to select multiple sequences to import. You can also drag and drop reads files onto the assembly project window. Also note that reads in a fastq file that have less than 10 bases, have mismatched quality and sequence lines, or have missing quality lines will be ignored. This filtering step is currently disabled for paired end reads.
Fastq files are added as a file based sequence collection. This stores a reference to the original file rather than importing and storing this file. This is done to save disc space, as fastq filesizes may be many gigabytes. If you move the original file the operating system may be able to keep track of the file but you may need to use the Locate button in the Assembly Project window to restore the new filepath.
By default if two reads files are selected this will be enabled. If three or more files are selected this will be disabled. However, it can manually be turned back on. The read files must be sequentially numbered so that when they are submitted the pairs will be together.. For example "READSFILE_A_1.fastq", "READSFILE_A_2.fastq", "READSFILE_B_1.fastq" and "READSFILE_B_2.fastq" will work for two pairs called READSFILE_A and READSFILE_B.