There are additional scripts that change many of the default options such as metaspades.py, plasmidspades.py, and rnaspades.py or these options can be set from the main spades.py script with the flags -meta, -plasmid, -rna respectively. SPAdes is actually written in python and the base script name is "spades.py". As always its a good idea to get a look at what kind of options the program accepts using the -h option. Now let's use SPAdes to assemble the reads. Tacc:~$ head your read pairs will be "separate" with the corresponding paired reads at the same index in two different files (each with exactly the same number of reads). Dataĭownload the paired end fastq files which have had their adapters trimmed from the $BI/gva_course/Assembly/ directory.
I analyzing this data on an idev node and then submitting the other data analysis for the bacterial genomes as a job to run overnight. Fortunately for this class, we can make use of the plasmid spades option to assemble and even smaller plasmid genome that is ~2000 bp long in only a few minutes. Unlike other times in the class where we are concerned about being good TACC citizens and not hurting other people by the programs we run, assembly programs are exceptionally memory intensive and attempting to run on the head node may result in the program returning a memory error rather than useable results. When it comes time to assemble your own reference genome, remember to give each sample its own compute node rather than having multiple samples split a single node.Īssembling even small bacterial genomes can be incredibly time intensive (as well as memory intensive as highlighted above).
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