Kaiju<\/a> is a program for the taxonomic classification of high-throughput sequencing reads, e.g., Illumina or Roche\/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from microbial and viral genomes.<\/p>\n Version 1.7.2 is installed on the CSF.<\/p>\n Details of the licence, restrictions, links to licence docs etc Please cite you use of this software using the reference:<\/p>\n We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings<\/abbr>.<\/p>\n Load one of the following modulefiles:<\/p>\n Please do not run Kaiju on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n You may<\/em> run the commands with the Note that kaiju is capable of downloading reference datasets and processing them to create the reference databases. This MUST<\/strong> be done as a batch job and you must inform the Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview Kaiju is a program for the taxonomic classification of high-throughput sequencing reads, e.g., Illumina or Roche\/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from microbial and viral genomes. Version 1.7.2 is installed on the CSF. Restrictions on use Details of the licence, restrictions, links to licence docs etc There are no restrictions on accessing the software on the.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-3705","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/3705","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=3705"}],"version-history":[{"count":4,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/3705\/revisions"}],"predecessor-version":[{"id":3710,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/3705\/revisions\/3710"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=3705"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
\nThere are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v3 license and all usage must adhere to that license.<\/p>\n\n
Set up procedure<\/h2>\n
\r\nmodule load apps\/gcc\/kaiju\/1.7.2\r\n<\/pre>\n
Running the application<\/h2>\n
-h<\/code> flag to see a list of flags accepted by the program. For example:<\/p>\n\r\nkaiju -h\r\nkaiju-makedb -h\r\n<\/pre>\n
kaiju-makedb<\/code> app how many cores your jobscript has requested (see below). By default kaiju-makedb<\/code> uses 5 cores so if in doubt, submit a 5-core job. See the examples below for how to run the various executables correctly.<\/p>\nSerial batch job submission<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd # Job will run from the current directory\r\n # NO -V line - we load modulefiles in the jobscript\r\n\r\n# Load the modulefile in the jobscript - use your required version\r\nmodule load apps\/gcc\/kaiju\/1.7.2\r\n\r\n# There are various commands that can be run\r\nkaiju -t nodes.dmp<\/em> -f db.fmi<\/em> -i reads.fastq<\/em> -j reads2.fastq<\/em>\r\n\r\n# When making a database (this is best done with a parallel job - see below)\r\nkaiju-makedb -t $NSLOTS -s source_db<\/em>\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Parallel batch job submission<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd # Job will run from the current directory\r\n#$ -pe smp.pe 8 # Number of cores, can be 2 -- 32\r\n\r\n# Load the modulefile in the jobscript - use your required version\r\nmodule load apps\/gcc\/kaiju\/1.7.2\r\n\r\n# There are various commands that can be run. The flag to say how\r\n# many cores to use varies from app to app so you should look this up.\r\n# $NSLOTS is automatically set to the number of cores requested above.\r\n\r\n# Some examples:\r\nkaiju -z $NSLOTS -t nodes.dmp<\/em> -f db.fmi<\/em> -i reads.fastq<\/em> ...\r\nkaijup -z $NSLOTS -f proteins.fmi<\/em> -i reads.fastq<\/em>\r\nkaijux -z $NSLOTS -f proteins.fmi<\/em> -i reads.fastq<\/em> ...\r\nkaiju-mergeOutputs -i in1.tsv<\/em> -j in2.tsv<\/em> .....\r\nkaiju-mkfmi filename<\/em> # Will read filename<\/em>.bwt and filename<\/em>.sa\r\nkaiju-mkbwt -n $NSLOTS args<\/em> filename<\/em>\r\nkaiju2krona -t nodes.dmp<\/em> -n names.dmp<\/em> -i kaiju.out<\/em> -o kaiju2krona.out<\/em>\r\nkaiju-convertNR -t nodes.dmp<\/em> -g prot.accession2taxid<\/em> -i nr<\/em>\r\n\r\n# When making a database\r\nkaiju-makedb -t $NSLOTS -s source_db<\/em>\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Further info<\/h2>\n
\n
Updates<\/h2>\n