SPAdes 3.6.0 \u2013 St. Petersburg genome assembler \u2013 is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads. Supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on single-cell and standard bacterial and fungal data sets.<\/p>\n
To send jobs to the queue you can use the<\/p>\n
send_spades<\/pre>\ncommand that asks few questions to configure the job.<\/p>\n
Performance<\/h2>\n
We have not measure any performance improvement or time reduction when using several cores in a standard calculation like:<\/p>\n
spades.py -pe1-1 file1 -pe1-2 file2 -o outdir<\/pre>\nWe recommend to use 1 core, unless you know that you can use better performance with several cores.<\/p>\n
More information<\/h2>\n
Web page of SPAdes<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"
General information SPAdes 3.6.0 \u2013 St. Petersburg genome assembler \u2013 is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads. … Seguir leyendo SPAdes<\/span>