ChangeLog.txt

-- Version 20201130
EDGE 2.4.0
* Update bcftools from 1.6 to 1.10.2
* Update samtools from 1.9 to 1.10
* Update racon from 1.3.1 to 1.4.13
* Add Python package lzstring, h5py
* Add biom format output for taxonomy classification module.
* Fix bug: data clean script in docker or symlink directory
* Fix bug: the fix mapping file Description column
* Fix bug: contig map to reference INDELs counting and show >85% mapped contig number
* Fix bug: RATT annotatiom embl format
* Update gottcha2 and pangia codes for corresponding database update
* Update megahit from 1.0.3 to 1.1.3.
* Update R from 3.3.2 to 3.6.3
* Update rgi from 3.1.1 to 5.1.0
* Update bowtie2 from 2.2.6 to 2.4.1
* Update bedtools from 2.19.1 to 2.27.1
* Update minimap2 from 2.10 to 2.16
* Update prokka from 1.13 to 1.14.5
* Update ncbi-blast from 2.5.0 to 2.10.0
* Update SPAdes from 3.11.1 to 3.13.0
* Update sratoolskit from 2.8.2 to 2.9.6
* Update JBrowse from 1.12.3 to 1.16.8
* Update Anaconda2 and Anaconda3 to 2019.10 and 2020.02
* Update lrasm from 0.1.0 to 0.3.0 which include new assembler wtdbg2 and (meta)flye
* Update gottcha dmd complier and use conda to install rapsearch2
* Add MaxBin tools for metagenome contig binning
* Add debug flag in auto_run script
* Add vcf filter options: -I and -r for alternative bases ration and INDEL depth support value
* Add Centrifuge taxonomy classification tool
* Update Kraken to Kraken-2.0.7
* Update Contig taxonomy classification from bwa to minimap2, perl to python
* Add CheckM v1.1.2 tool for assessing the quality of metagenome Binning
* Add AntiSmash v4.2.0 tool for secondary metbolite analysis
* Add QIIME2 pipeline and installation/requirement 
* Add script to extract VF/AMR protein
* Add "reference" column support for batch submit input excel file
* Add Chromium v75.0.3767.0
* Add Unicycler 0.4.8 for hybrid assembly
* Add Pilon 1.2.3
* Add Seqtk 1.3
* Add slurm scheduler support
* Add jq for json file query and quick dynamic search
* Add Align Trim for primers trim by BED coordinates
* Add Samclip to filter large clipped aligned reads
* Add primer track in JBrowse if BED file is used
* Allow upload bed file and add BED format check

EDGE GUI 2.4.0
* Add Ploidy option for Variant calling
* Add anchor link in the result page to quick accession module result
* Add one more line for LibreOffice xlsx format check
* Adjust mobile portrait width for front page
* Fix bug: the reset function disabled show on the registration iframe page.
* Add Binning tag in Assembly and Annotation Module
* Add CheckM switch in Assembly and Annotation Module
* Update Taxonomy tool result display by user select options
* Add extract reads fastq for Kraken result
* Add Secondary Metabolite Analysis Annotation
* Update Qiime to version 2
* Add wtdbg2 and (meta)flye long reads assembly algorithm option
* Add Unicycler option for assembly
* Hover to show accession id for genome search result list
* Update final_report.pdf to match with web based summary result page
* Add primer trim method switch, FaQCs or Align_trim
* Add the PCR deduplicates switch for consensus
* Add the MaxClip option


Database:
GOTTCHA2: update to Refseq90
Kraken2: New db from Refseq (as of Dec 20, 2018)
MiccrDB: New db from Refseq (as of Dec 20, 2018)
CheckM_DB: source https://data.ace.uq.edu.au/public/CheckM_databases/ (2015 Jan)
CARD: update to 3.0.0 
QIIME2 amplicon: Greengeen 13_8, SLIVA 132, Fungal ITS version 8.0 trained by scikit-learn 0.20.2

-- Version 20180829
EDGE version 2.3.1
* fix bug: blank SRA accesion variable 
* Add comma separated single reads support for batch submit
* Add script to update existing projects status, runtime, submission time
* Add contig taxonomy classification info (species) into JBrowse annotation gff track 
* Assign HOME to EDGE_HOME when not using regular user runing PanGIA
* Update samtools from 1.6 to 1.9
* Auto Adjust bwa alignment score by reads length for PanGIA pipeline.

EDGE GUI 2.3.1
* fix bug: corrupted gz file using Upload function

-- Version 20180724
EDGE version 2.3.0
* Update Kraken version from 0.10.4 beta to 1.0
* Update Metaphlan from 1.7.7 to 2.7.7
* Add global numCPU option for runReadsToGenome and runReadsToContig scripts
* Add Qiime taxonomy plot bar chart and alpha diversity analysis for only one sample
* fix bug: fasta header correction for consensus pipeline
* fix bug: project rerun in docker container. remove some system call
* update PyPiRt version from 0.3 to 0.3.2. ID to SampleID.

EDGE GUI version 2.3.0
* Add Take Notes Button in result page
* Update userManagement API to return all fields of project page in json to speed up page loading
* Update Metaphlan to Metaphlan2
* Multiple SRA number input with comma separated
* Add Phred Quality Offset for QC module
* fix bug: project report selection

Database:
* MiniKraken database update from version 2014 to 20171101 8GB version.
* Add Metaphlan2 database

-- Version 20180618
EDGE version 2.2.0
* Update pangia from 2.4.5 to 2.4.10
* Add changes for modules when Nanopore Reads option is on.
* Add Test Case for Nanopore data
* Update prokka version from 1.11 to 1.13
* Update barrnap version from 0.4.2 to 0.9
* Add cmake 3.6 and racon v1.3.1 software for compling and assembly
* fix bug : minimize backtick used in edge_action.cgi, runDETEQT in config.tmpl
* fix bug: qsub error check for taxonomy classfication module 
* fix bug: unknown accesion for genbank to fasta conversion
* fix issue: sra download with ssl self-certificate or insecure connection
* fix bug: gottcha bwa opiton error
* fix bug: PiReT exp design parsing and load correct pirect env
* fix bug: Phylogeney analysis if only provide geonome files

EDGE GUI version 2.2.0
* Add Nanopore Reads Options
* Add app-like front page
* Add auto turn on if host file/primer file input selected
* Add parameter in the Piret Result and fix typo, datatable
* Add number sequence fragments check for reference based analysis
* Auto turn on hose removal if host selected from the list
* Add color spectrum for user custom theme color
* Add dynamic table for PiReT differnetial expression significant genes
* Add check process status for extract reads fastq
* Add cache edge info/projectlist page. 
* Add check status for long process actions to avoid timeout
* Make action "Delete" and "Empty" run in background to avoid timeout
* Use json for projectspages table to speed up the page loading process
* Add Password requirement for user registration. (Must contain at least one
number and one uppercase and one lowercase letter and one special character,
and at least 8 or more characters.)
* fix bug: project report \x0000 null character and html tag invalid
* fix bug: jquery mobile dialog error on extract reads/contigs
* fix bug:Fixed read number at comparative table for pangia

-- Version 20180502
EDGE version 2.1.1
* Add SSL configuration example
* fix bug: Cannot find file name with many dots of PhaME input genome
* fix bug: FaQCs polyA flag expected no argument
* support uge for taxonomy classification module

EDGE GUI version 2.1.1
* fix bug: reconfiguration action and submit
* fix bug: PiReT tab to json script
* fix bug: piret directory submit using absolute path. Piret result page update
* fix bug: Safari does not like window.open in ajax sucesss.
* fix bug: autorun failed introducd by update of edge_submit.cgi, need new line for the print message to log 


-- Version 20180425
EDGE version 2.1.0
1. Add minimap2, a long noisy read aligner
2. Update samtools/bcftools from 0.1.19 to 1.6 
3. Update FaQCs to 2.07 and allow process long reads
4. Add alinger option for PhaME. support bowtie/bwa/minimap2
5. Update MetaComp to 1.0.2.
6. Add bokeh server check script for PanGIA visulization, pangia-vis-checker.sh
8. Update pangia from 2.3.2 to 2.4.5
9. Update tbl2asn
10. Update targetedNGS tool and rename to DETEQT, and update its test case
11. Get proxy setting from system for SRA download
12. Remove .complete_report_web for import script
13. Check symlink for pangia-vis, JBrowse and Opaver data.
14. Add PyPiReT Pipeline (https://github.com/mshakya/PyPiReT) Pipeline for Reference based Transcriptomics.
15. Add long reads assembler pipeline (minimap2 -> miniasm -> racon, https://gitlab.com/chienchi/long_read_assembly)
16. Update Anaconda3 from 4.1.1. to 5.1.0
17. Add NanoPlot v1.13.0, Plotting scripts for long read sequencing data. (https://github.com/wdecoster/NanoPlot)
18. Add Porechop v0.2.3, a tool for finding and removing adapters from Oxford Nanopore reads. (https://github.com/rrwick/Porechop)

EDGE GUI version 2.1.0
1. Allow batch submit with http/ftp for input reads
2. Add option to use only joined PE reads for downstream analysis
3. Add diamond and pangia heatmap from MetaComp.
4. Add minimap2 GUI option (mapping to contigs/reference) for nanopore dataset
5. Add security of Apache configuration and bokeh proxy service for pangia-vis
6. Add file content check of upload files.  
7. Add messages when NCBI_Genomes are not synced with ref_list.json file
8. Add project owner in the result page
9. Remove output path from GUI
10. Add javascript disabled msg
11. Get userType from server side
12. Security Patch on all cgi scripts by sanitize all input. 
13. Redirect to register page when social login failed.
14. Reset button on select menu
15. Check session for upload. Remove some system call
16. Add load num for project pages
17. Use xlsx2csv for batch excel file process
18. Sanitize batch sumbit input
19. Allow upload gff fomrat text file
20. Rename TargetedNGS to DETEQT
21. Add batch project info into config.json for reconfig function.
22. Add Beta version of Pipeline for Reference based Transcriptomics.(PyPiReT)
23. Add LRASM assembler (long reads assembler)

EDGE docker:
https://hub.docker.com/r/bioedge/edge_dev/
1. Developed docker_deploy scripts

Database:
Full Kraken database is available on ftp://ftp.lanl.gov/public/genome/EDGE/full_kraken_db/
User can use it as custom kraken db. The database is large (155G after unzip) and using it requires ~150 GB memory too.


Bugs fixes: reconfig with unexpected behavior, edge_actions.cgi sequential actions on multiple projects, 
            the null chcaracter in the config.txt cause error on runPipeline, fix link for example data set
            ...

-- Version devel 2.0.0
2018/01/16
1. Add mummerplot for contig to reference dotplot
2. Add .gz support for provided contigs fasta
3. Convert upload text file newlines to UNIX format.
4. Update Pathogen database and pathogen identification script to apply on gottcha2 result
5. Update/Check metadata with SRA id and automatically retrieve metadata info from EBI ENA API
6. Chagne gi to taxonomy mapping to acc to taxonomy mapping
7. Kronatools from 2.6 to 2.7
8. Track uge cluster pending jobs
9. Add gbff extension for genbank file
10. Publish video tutorial series on Youtube (https://www.youtube.com/playlist?list=PL7DNo6h5wJsTh2l2GK3N86Imb-9fYQFfH)
11. Change reads to reference mapping algorithm: from mapping reads to concatnated reference To reads to reference individually.  
12. Update matplotlib to 2.0.0 for Qiime Compatible
13. Add Pacbio CCS reads quality encoding format check
14. QC: raise the opt_q=20 if data is NextSeq
15. Wrap R packages and Python (Anaconda2 and Anaconda3) Packages for no internet installation.
16. Add PanGIA Bioinformatics Pipeline
17. Update SPAdes from 3.7.1 to 3.11.1 
18. R version 2.15.3 to 3.3.2
19. Add metagenome option for prokka annotation 
20. Add wget as download interface for sra/file download
21. tbl2asn from 24.9 to 25.3
22. sratoolkit from 2.5.4 to 2.8.1
23. Update MetaComp to v1.3 and add gottcha2 comparison scripts
24. Resume failed taxonomy profling result when project rerun.
25. Remove forking function in microbial_profiling.pl 
26. Add edgeui_result_table_rows variable in sys.properties for control result page contigs table rows
27. sra2fastq.pl updates to v0.5: 1) auto switching download site from NCBI-SRA/EBI-ENA/DDBJ; 2) separate http and ftp proxy
28. Update adapter trimming algorithm. if more than one adapter in a read, the read is tosed.
29. Separate autorun feature from edge_info into a cronjob
30. Add cache file for the finished projectpage info. 
31. Sort taxonomy tree dendrogram alphabetically 
32. Publish EDGE_ABCs.pdf document and link on the homepage
33. Add default max (20) and min(3) input genomes check for reference mapping and phylogenetic analysis
34. Add CarioSVG package for svg to pdf conversion.
35. Add Python3 support 
36. Using RGI for Specialty Genes Detection module
37. Added max_num_jobs to allow control over how many jobs can be submitted
38. Add error_notification switch 
39. Allow manual proxy setup
40. Add TargetedNGS pipeline
41. Add script to print tool version
42. Add contig only input function
43. Add omics pathway viewer tool 
44. Update FaQCs to version 2.06. speed up 10x
45. Support gz on provided contig file
46. Reduce memory usge for runReadsToGenome to large/many Genomes
47. Add consensus pipeline
48. Add Diamond aligner version 0.9.10
49. Use JSON::XS to speed json decoding 
50. Add meta data in EXCEL(xlsx format) support for qiime pipeline
51. Add consensus JBrowse Track. 
52. Update JBrowse from 1.11.6 to 1.12.3. 
53. Add find repeats (self_nucmer) script and add JBrowse tracks for repeats

GUI update:
1. Add NCBI link for reads to reference accession
2. Add Phred+33 or Phred+64 GUI options for Qiime
3. Add extract mapped reads fastq or mapped contig fasta function in the result table
4. Make error msg read easier on the result web page
5. Check browser localstorage support
6. Add PanGIA Bioinformatics Pipeline option for taxonomy profiling
7. Check online with internet before loading google maps api for metadata
8. Add rnaSPAdes, plasmidSPAdes options for SPAades assembler 
9. Add Reconfig/rerun project action (beta)
10. Sample Metadata actions: Add. Edit. Delete, Export as Excel
11. Share metadata/pathogens button for surveillance
12. Hide project display action
13. Add alt-click projectname to open in a new tab in project page and mouse over reminder
14. Add custom db input for reads taxonomy profiling 
15. Add polyA trim option.
16. Add user defined metadata input textfield. 
17. Add tooltips for many parameters 
18. Add project name banner beside username and as a button that can switch to project report immediately (no-loading).
19. Improved mobile compatibilities
20. Icons updated for mobile devices for making an app icon on the mobile device (see https://edge.readthedocs.io/en/develop/troubleshooting.html)
21. Add select all checkbox for the project page
22. Add progress bar to report page.
23. Update Specialty Genes Detection module result display
24. Performance improvement for listing projects and project report
25. Add edge site information form when first time EDGE use for metadata usage
26. Add TargetedNGS pipeline
27. Add splitrim minimum quality level option.
28. Add Stitch Paired End Reads function in Pre-processing module
29. Add Contig only Input for EDGE and GUI button
30. Allow gbff extension upload
31. Add KEGG plot from prokka result
32. Add Options for Consensus pipeline
33. Add Diamond protein based taxonomy classifier
34. Add security check for uploading files, need session id and targetDir
35. Add chart_type option for qiime pipeline
36. Add multiple projects report pipeline
36. Redesign the Gene Family module output table.

New Databases;
GOTTCHA2: RefSeq-Release81.Virus, RefSeq-Release81.Bacteria
PanGIA: NCBI_genomes_111216_p_GRCh38.fa 
Diamond: RefSeq_Release83.nr_protein_withRefSeq_viral_102317.protein.faa.dmnd
Host bwa index:  pig, sheep, cow, monkey, hamster. and goat.

Bugs fixes: resume taxanomy profiling result excel report,  JBrowse Error reading name store, qiime input check, download project zip file.
             tax id not exist in the NCBI taxonomy dump, trim 5 end and trim 3 end does not work, concatenate reference fasta with newline,
             Multiple genome reference input check , dynamic search box on dialog and popup, etc.

-- Version 1.5
2016/08/25
1. User management allows to configure email notification 
2. Check host file writable for bwa index and reuse the index if it existed.
3. Adjust NextSeq trimming quality to q=16
4. Allow user logged in until CGI session expired
5. QC script will report invalid gzip format issue
6. R version 2.15.3 to 3.2.2, 
7. KronaTools version 2.4 to 2.6, 
8. Bowtie2 2.1.0 to 2.2.6, 
9. gridExtra version 0.9.1 to 2.0.0
10. Upgrade sratoolkit version from 2.4.4 to 2.5.4 which support proxy setup and make sra2fastq.pl work on pacbio and solid platform.
11. SPAdes from 3.5.0 to 3.7.1 (with meta flag for metagenome)
12. Add project name at the right bottom of final report pdf
13. Add Computational resource check before preforming any action or submit new job.
14. Clean intermediate files script for cron jobs set up. If cron job set up, EDGE will pop up reminding message
15. Utility scripts to convert bam to fastq and extract fasta by taxonomy from contigs profiling result
16. Update project dir by using secure code instead of project id
17. Add email functions when job complete or shared to others
18. Separate [system] configruation from edge_config.tmpl into sys.properties.
19. Add bam_to_fastq_by_taxa.pl script to extract fastq from gottcha result by taxonomy
20. Add edgeamdin acoount info into sys.properties and remove them from embeded code
21. Make the example apache configuration file ready for copy with EDGE installation script
22. Add a hash table on host file to avoid duplication
23. Add ShortBRED and RAPSearch thirdparty tools and installation scripts.
24. Add ShortBRED function for Antibotic resistance genes and Virulence Genes and simple ouptut count table
25. MEGAHIT metagenome assembler.
26. (univa) UGE cluster submission support (alpha test)
27. Qiime amplicon analysis pipeline for 16s/18s/ITS data (Greengenes/SILVA/ITS)
28. Allow the multiple runs/lanes (with or without duplicate barcodes) into the Qiime amplicon analysis pipeline
29. Add MetaComp package (https://github.com/seninp-bioinfo/MetaComp. Pavel Senin).
30. Add module configuration on/off in the sys.properties
31. Add email_recipient in sys.properties that email will send not only to project owner but to the email_recipients here.
32. Added import script and helper perl script, imports project into um from tar.gz
33. Rename contigs.fa to $projectname_contigs.fa which can be setting up for phylogenies. 
34. Add GOTTCHA2 compatibility
35. Add sample metadata module and pathogen detection module
36. Update FastTree from 2.1.7 to 2.1.9 and complied with double precision
37. Add data cleanup option for the runPipeline script to remove .sam .bam .gz .fastq .fq. tgz files after run finished
38. Add 17 module/unit tests
39. Add "force" option to install all tools locally in the INSTALL.sh
40. Concatenate gff files for PhaME module and modify gff coordinate for mutliple segments reference
41. Update PhaME: the phylogeny analysis module
42. Improve edge report performance

GUI update:
1. GUI: Skip hidden files while selecting files
2. GUI: Scroll up button
3. GUI: download project button, which will compress the project directory but exclude bam, sam, fastq , gz files
4. GUI: Add aligner and aligner options for mapping reads to contig/reference
5. GUI: Add Bootstrap option for Phylogenetic analysis
6. GUI: option to extract unmapped/mapped reads from reads mapping to contigs/reference
7. GUI: Add extract reads from gottcha/bwa result by taxonomy
8. GUI: options for MEGAHIT metagenome assembler
9. GUI: A new navigate menu for Qiime analysis pipeline
10. GUI: /edge_ui/?proj=xxxxxxxxx  url query works on the secure project code.
11. GUI: A new Specialty Genes Detection module for EDGE pipepine.
12. GUI: Mutliple project selection with actions drop list. Delete, Share, Publish, Archive, Compare Gottcha result.
13. GUI: Result page with Contig table view for JBrowse link and Blast NT function.
14. Brighter highlighting of the job that being displayed in the left project bar
15. Add project list number show limit but still searchable for hiddent list. This will speed up when user have hundreds projects
16. Add rename project name /desc action
17. Add empty/interrupt/empty actions for mutiple projects. allow interrupt on queue jobs
18. Add define gap action to dynamic display gap analysis result table
19. Add plus button for adding more reference genome select box.
20. Change project page action drop list to buttons

Database update:
1. GOTTCHA db version v20150825

Bugs fixes: batch submit bugs, tree view cutting issue, upload function fail when user management system is off, overly running taxonomy profiling tools in parallel... etc.

-- Version 1.1
2015/08/19
1. Add size limit to contig for annotation ( default 700bp)
2. Display heatmap at community profiling section
3. Add script to 1. convert newick tree to phyloxml 2. midpoint reroot 3. add annotation for url and descriptions
4. Updated JBrowse to 1.11.6. 
5. Improved tree and tooltip visulization.
6. Testing/documentate installation on CentOS 6, CentOS 7 and Ubuntu 14.04
7. Support fastq.gz input
8. Added project managment functions/widget, resource monitor widget
9. Added queuing function, auto start queued projects
10. Update GOTTCHA module to 1.0b
11. Update host removal script to output host fastq file and using similarity cutoff instead alignment score.
12. Add selectmenu for choosing host, reference genomes ( Support multiple selection )
13. Update Virus Database of GOTTCHA
14. Add paired reads check. If failed, will use them as single end reads
15. Add buttons to add paired-end/single-end fasta input field in Advanced option
16. Add Batch submit 
17. Reorganized output directory structure.
18. Add RAxML tree builder
19. Remove 0% coverd contigs
20. Add Select (ref)  genomes, SRA input function for SNP phylogeny
21. Add input from NCBI SRA function and sratoolkit
22. Add Contig classifictaion function by BWA. Remove Blast section of EDGE Gui
23. Add LCA function to contig classifier
24. Check duplicate input error
25. Add rank switch to the summary of taxonomy classification.
26. Add User Management System
27. Replace GOTTCHA databases to xHUMAN3x databases.
28. Update bwa version from 0.7.9 to 0.7.12. 
29. Add RATT annotation option on EDGE GUI
30. Allow user to add other genomes in Phylogenomic analysis
31. Correct INDEL count number in contigMapToRef
32. Add all NCBI RefSeq to reference selecting menu.
33. Server-side session implemented. Session expiration detection and deletion.
34. Reference selection includes annotations. (NCBI_genomes.tar.gz)
35. Add social network login function (Facebook, google, windows live, Linkedin)
36. Add SPAdes 3.5 assembler (can input Pacbio/Nanoport for gap closure) and user provided contigs options to skip asssmebly
37. Update prokka to 1.11
38. Add tooltip and Mission popup
39. Add NextSeq platform check and automatically adjust opt_q to 15 if opt_q < 15 for QC module
40. Add Upload Files Function. Max file size is '5gb'. Allowed File types are fastq, fasta and genbank and can be in gzip format. Files will be kept for 7 days.
41. GOTTCHA with plasmid and read count
42. Remove metaphyler-srv 
43. Multiple improvements and bugfixes

-- Version 1.0
2014/08/26
1. * Jquery edge_ui implementation for input and output html
2. Allow multiple host removal
3. Several bugs fixs.
4. Add SNP phylogeny 
5. Add primer Tm and length range to primer design
6. Add lazyload to improve result page loading performance
7. Manual created online at edge.rtfd.org
8. Add Contig Blast result
9. Remove Perl Tk GUI and package
10. Bugs fixed.

-- Version 0.5
2014/04/10
1. Add GOTTCHA profiling to
2. Add JBrowse
3. Add function to generate radar chart
4. Add a python script for starting a local web host
5. Update main script and gui to start the http localhost when job processed.
   and Auto lauch result html page when job finishd.
6. Add script generating JBrowse tracks.
7. Add "debug" option to microbial_profiling.pl. 
8. Allow most of modules to on/off switch
9. Update bwa from 0.7.5a to 0.7.9
10. Update parallel version
11. Update prokka from 1.7 to 1.9
12. Add barrnap for rRNA prediction
13. Add adapter trimming and phiX filtering options for QC step
14. Remove File::Tee dependency and fix program call path issue
15. Update INSTALL script to more control options
16. add Metascope, FastTree and RAxML tools
17. add output HTML munger in runPipeline

-- Version 0.4
2014/2/10
1. Update bwa from 0.7.5a to 0.7.7
2. Add Version into process log and bug fix on annotation flag
3. Fix a major bug on gui when output directory is not existed3.
4. Comment out MEGAN 
5. Remove redundant ktImportBWA script 

-- Version 0.32
2013/12/18
1. Replace MEGAN tree plot script with custom Perl scrips/modules.
2. Add krona_portable.pl script to generate portable krona html and fix runReadsToGenome.pl when input non-alphanumeric reference name
3. Add process log and error log into project output directory
4. Fix bugs on phageFinder and pdf cat when there is no protein annotation result.
5. Add annotation check box and function
6. Add bwa mapping reads id to Taxonomy lookup text file (.classification)
7. Add contig id to Taxonomy lookup text file (.classification)

-- Version 0.31
2013/12/11
1. Improve primer Adjudication module with Tm calculation and sorting.
2. Add kraken-0.10.2-beta thirdParty software for taxonomy classification
3. Update the Perl GUI interface
4. Add Annotation stats output
5. Add existing output directory detection and warning.
6. Add README.pdf documentation
7. use bitbucket (git) for version control


-- Version 0.3 --
2013/11/10
1.Improve primer Adjudication module for Novel pathgen
2.Improve primer Validation module to allow checking multiple primer pairs in fasta 
  and IUPAC degenerate base check 
3. Update the Perl GUI interface

-- Version 0.2 --  
2013/09/10
For EDGE use case 2:  Extreme Symptom
Adding modules
1. Annotation: Prokka or RATT
2. Phage finder
3. Taxonomy analysis
4. novel contigs/regions Analysis
5. SNP/INDEL analysis

-- Version 0.1 --   
2013/06/01
For EDGE use case I: Assay Failure detection
Have modules:
1. Data QC
2. Host Removal QC 
3. IDBA Assembling
4. Map Reads To Contig
5. Map Reads To Reference Genomes
6. Map Contigs To Reference Genomes 
7. PCR Assay Validation and Adjudication