xiangrong131 / diamond

Utilizes Diamond to generate BlastX data from sequence reads

Diamond

This program utilizes Diamond to generate BlastX data from sequence reads. The default reference database used in this analyses is Swiss-Prot and will automatically be downloaded for use. The Diamond output files (.dout) are in BlastX format and Swiss-Prot ids are extracted from the results (.ids). The Swiss-Prot ids are assigned NCBI taxonomy ids (.taxid). Counts are then generated for both taxonomy (tax.count) and Swiss-Prot ids (id.count). See "Expected Results" section for examples of output files.

If you want to use a reference other than Swiss-Prot, a Diamond database must be generated.

$ diamond makedb --in nr.faa -d nr

This program is optimized for the default settings which uses Swiss- Prot reference database. If using the default settings, the above command is not necessary.

Before Start:

A file named 'list' needs to be created in the directory containing your Fasta/q files. The program will read 'list' in order to know what files need to be analyzed. Below is an example of how 'list' could be created:

$ cd $FASTA_DIR
$ ls
file1.fa   file2.fa   file3.fa
$ ls *.fa > list
$ cat list
file1.fa
file2.fa
file3.fa

Instructions:

1. Edit the VARIABLE DECLARATION section at the top of submit.sh to include the paths for the FASTA_DIR (location of fasta files and 'list') and DIAMOND_DIR (location of Diamond executable). Other variables can be edited as needed such as THREADS (# of CPUs). PRESETS only need to be changed if you are not using the default Swiss-Prot database.

2. Edit PBS ALLOCATIONS section at the top of diamondx.sh (found in script directory). Here is an example of a complete PBS ALLOCATIONS:

   #---- PBS ALLOCATIONS ----

   #PBS -W group_list=bhurwitz #PBS -q standard #PBS -l select=1:ncpus=4:mem=15gb #PBS -l pvmem=12gb #PBS -l place=pack:shared #PBS -l walltime=24:00:00 #PBS -l cput=24:00:00 #PBS -M [email protected] #PBS -m bea

Note that group_list, -q standard, and -M email, should be edited to include your group name, queue type, and email respectively.

3. Execute submit.sh

   $ ./submit.sh

Expected Results:

Diamond Blast Output (.dout) -

[jamesthornton@service1 diamond_out]$ head IonXpress_017.dout
3932-6  sp|Q99959|PKP2_HUMAN    72.7    33  9   0   106 8   472 504 4.4e-07 53.9
3932-6  sp|Q05481|ZNF91_HUMAN   80.0    30  6   0   90  1   1159    1188    1.7e-06 52.0
3932-6  sp|Q7Z5D8|NANGN_HUMAN   76.7    30  7   0   105 16  332 2.2e-06 51.6
3932-6  sp|Q86V71|ZN429_HUMAN   74.1    27  7   0   97  17  648 674 9.2e-05 46.2
5017-5  sp|B2RM62|UVRC_PORG3    60.0    40  16  0   5   124 55  94  1.8e-06 52.0
5017-5  sp|Q7MTG8|UVRC_PORGI    60.0    40  16  0   5   124 54  93  1.8e-06 52.0
5017-5  sp|Q04EZ7|UVRC_OENOB    55.0    40  18  0   5   124 53  92  1.2e-05 49.3
5017-5  sp|B3E394|UVRC_GEOLS    58.3    36  15  0   17  124 55  90  4.5e-05 47.4
5017-5  sp|Q8REL0|UVRC_FUSNN    55.0    40  18  0   5   124 48  87  4.5e-05 47.4
5017-5  sp|Q14I60|UVRC_FRAT1    55.0    40  18  0   5   124 59  98  2.2e-04 45.1

Swiss-Prot ID list (.ids) -

[jamesthornton@service1 diamond_out]$ head IonXpress_017.ids
PKP2_HUMAN
ZNF91_HUMAN
NANGN_HUMAN
ZN429_HUMAN
UVRC_PORG3
UVRC_PORGI
UVRC_OENOB
UVRC_GEOLS
UVRC_FUSNN
UVRC_FRAT1

Taxid Assignment (.taxid) -

[jamesthornton@service1 diamond_out]$ head IonXpress_017.taxid
PKP2_HUMAN = 9606
ZNF91_HUMAN = 9606
NANGN_HUMAN = 9606
ZN429_HUMAN = 9606
UVRC_PORG3 = 431947
UVRC_PORGI = 242619
UVRC_OENOB = 203123
UVRC_GEOLS = 398767
UVRC_FUSNN = 190304
UVRC_FRAT1 = 393115

Taxid Counts (tax.count) -

[jamesthornton@service1 diamond_out]$ head IonXpress_017_tax.count
9565    16
378806  4
135720  9
9595    91
138119  20
1245    2
9833    37
323850  33
9546    1
224324  106

Swiss-Prot ID Counts (id.count) -

[jamesthornton@service1 diamond_out]$ head IonXpress_017_id.count
TRMFO_RHIL3 2
GCDH_MACFA  2
RL16_MYCPA  1
LOLD_XANOR  1
XYLG_RALSO  1
FABZ_VEREI  1
PANB_NITOC  1
UVRC_FRATM  2
SECA_GEOMG  3
Y1095_PORGI 1

For more information on Diamond see the user manual at http://ab.inf.uni-tuebingen.de/data/software/diamond/download/public/manual.pdf

Diamond publication can be found here: http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3176.html