Srst2 - Revision history

Rf at 13:24, 16 January 2017

2017-01-16T13:24:44Z

2017-01-16T13:23:29Z

2017-01-12T10:59:03Z

2017-01-12T10:57:39Z

2016-12-14T14:50:25Z

2016-12-14T14:46:36Z

2016-12-14T14:44:19Z

2016-12-14T14:43:37Z

2016-09-23T16:29:34Z

2016-09-23T16:22:17Z

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 * '''--input_pe''', after this the program expects to see any number of pair-wise ordered fastq files. By default, it prefers to have the name of each member of a pair ending in "_1.fastq.gz" and "_2.fastq.gz". It's quite likely your pairs of fastq files are not named in that way. You can however define the <suffix>.fastq.gz for the srsts2 program with the '''--forward''' and '''--reverse''' options. For example, in the case of trimmomatic-trimmed pairs which have their own particular naming scheme, you would use "--forward _forward_paired" and "--reverse _reverse_paired"
 * Up to '''--save_scores''' the command line clearly takes in input fastq files, and defines an output directory. The final three options are now explained.
-* '''--mlst_db''', this is for specifying the MLST database, a file of fast sequences for each of the variants of the housekeeping gene. The number of varaitns for each is unsurprisingly different. '''adk7''' has some 580, while '''fumC''' has over 800 variants.
+* '''--mlst_db''', this is for specifying the MLST database, a file of fast sequences for each of the variants of the housekeeping gene. The number of variants for each is unsurprisingly different. '''adk7''' has some 580, while '''fumC''' has over 800 variants.
 * '''--mlst_definitions''', defines a file give all the types in terms of their combination of variant number of the seven housekeeping genes.

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 The multi-pair processing command-line is as follows:
-  srst2 --input_pe ERR024082*.fastq.gz ERR028690*.fastq.gz ERR024619*.fastq.gz --output shigella3 --log --mlst_db Escherichia_coli#1.fasta --mlst_definitions ecoli.txt --gene_db ARGannot.fasta
+  srst2 --input_pe ERR024082*.fastq.gz ERR028690*.fastq.gz ERR024619*.fastq.gz --output shigella3 --log --mlst_db Escherichia_coli#1.fasta --mlst_definitions ecoli.txt --gene_db ARGannot.fasta -mlst_delimiter '_'
 Note how the output prefix is shigella3, our third processing command-line.

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 * first step:<pre>&#10;getmlst.py --species "Streptococcus pyogenes"</pre>
 * to launch parallel instance of srst2 on each of the pairs:<pre>&#10;qsub_srst2.py --input_pe *.fastq.gz --output <choose_a_name_for_output> --queue lowmemory.q --other_args "--mlst_db <name_of_species>.fasta --mlst_definitions <name_of_species>.txt --gene_db ARGannot.fasta --mlst_delimiter '_'"</pre>
 = Watchouts =

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 * The ARG-ANNOT database can be downloaded at the following [http://www.mediterranee-infection.com/article.php?laref=282&titer=arg-annot link]
 * first step:<pre>&#10;getmlst.py --species "Streptococcus pyogenes"</pre>
 * to launch parallel instance of srst2 on each of the pairs:<pre>&#10;qsub_srst2.py --input_pe *.fastq.gz --output <choose_a_name_for_output> --queue lowmemory.q --other_args "--mlst_db <name_of_species>.fasta --mlst_definitions <name_of_species>.txt --gene_db ARGannot.fasta --mlst_delimiter '_'"</pre>

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 * The ARG-ANNOT database can be downloaded at the following [http://www.mediterranee-infection.com/article.php?laref=282&titer=arg-annot link]
 * first step:<pre>&#10;getmlst.py --species "Streptococcus pyogenes"</pre>
-* to launch parallel instance of srst2 on each of the pairs:
+* to launch parallel instance of srst2 on each of the pairs:<pre>&#10;qsub_srst2.py --input_pe *.fastq.gz --output <choose_a_name_for_output> --queue lowmemory.q --other_args "--mlst_db <name_of_species>.fasta --mlst_definitions <name_of_species>.txt --gene_db ARGannot.fasta --mlst_delimiter '_'"</pre>
 = Watchouts =

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 A smaller number of loci, i.e. 7, are used to divide up the population.
-These loci come in the shape of entire housekeeping genes that all the species and isolates are bound to have.
+These loci come in the shape of housekeeping genes that all the species and isolates are sure to have.
-This proves to be robust unlike the alternative of assembling the genomes ''de-novo'', which, when dealing with 100 or 1000 bacterial genomes (a typical workload in bacteria), is a major issue.
+Typing this way proves to be robust unlike the alternative of assembling the genomes ''de-novo'', which, when dealing with 100 or 1000 bacterial genomes (a typical workload in bacteria), robustness is a major issue.
 = Watchouts =

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   --mlst_delimiter '_'
-will define the underscore as the delimiter.
+will define the underscore as the delimiter. The underscore seems alot more common than the dash, but unfortunately the default for srst2 is the dash.
 == output files ==

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 A somewhat diverting option is
-* '''-output''' which actually is for giving the the prefix name for the various files that will be output. '''Beware''' this is not a directory name, merely a prefix added to the names of the output files.
+* '''-output''' which actually is for giving the the prefix name for the various files that will be output. '''Beware''' this is not a directory name, merely a prefix added to the names of the output files, so you will still get a lot of clutter in your current working directory.
 The end of the output from this command will give a idea as to how rich the results, and they will be poor if there are few read pairs that aligned. Thsi will be true in the case of the example's ERR024070 read pair, which was very low coverage. A good deal of files are also output from this stage: