PHASIS (v3) - PHAS Inspection Suite

Note: PHASworks/PHASter is now PHASIS

See wiki for more information on installation, usage and description of results.

Enhancements:

phasdetect (previously named as phaser):

• Added a new index integrity checker to accommodate different index formats from the Bowtie and to ensure the completeness of genome index
• Improved core assignment, critical improvement for machines with eight cores or less
• Fixed a regression affecting analyses for large genomes using index with 64-bit numbers [25-Apr-2015]

phasmerge (previously named as collapser):

• Added the annotation function, which enables matching of PHAS loci to genome annotations; and can be used to identify PHAS transcripts when supplied with GTF file for transcriptome assembly by mapping it to genome
• Added the compare mode, which allows comparison between two different PHAS summaries
• Updated the runType modes for better speed optimization
• Improved a couple of functions to maximize parallelization - significant speed gain over previous version

phastrigs (previously named as revFerno):

• Added a new ‘search space’ setting to define search space for triggers - it takes values in PHAS cycles i.e. value of 3 will scan for trigger site three phased positions to left and three to right of P1
• Minor bugfixes

And,

• complete dependency checks before running tool(s)
• better error handing

Report issues here
Check wiki here
Track progress on bug fixes and new features here

phasTER

See wiki for more information on installation, usage and description of results.

Enhancements:

phaser

• Now accepts sRNA files in FASTA format, in addition to flat file format
• Optimized for faster index preparation and sRNA mapping to genome and transcriptomes
• Now includes three runType modes for Genomes, Transcriptomes and Scaffolded genomes

collapser

• New and faster algorithm for comparing PHAS loci from multiple libraries and confidence levels
• Better optimization of PHAS loci co-ordinates for improved trigger prediction by revFerno
• Reports 10% or more (good quality) phased loci compared to earlier version
• Improved matching of PHAS loci from different libraries and reporting of results
• Better selection of p-value for collapsing if no input supplied by user
• Generates a new result file "*clust.txt" which includes PHAS clusters from different libraries, useful for manual curation and downstream analyses

revferno

• Superlatively fast compared to earlier versions due a new workflow
• Super simplified workflow with new -mode option that includes an auto mode
• Automatic mode eliminates the need for running sPARTA externally for target prediction or PARE (or Degradome) validation
• MicroRNA triggers for PHAS loci can be predicted or PARE (or Degradome) validated, directly in automatic mode
• Identifies trigger for 15- 25% more PHAS loci compared to earlier versions
• Accepts PARE data in both FASTA or flat file format with tags and counts separated by tab

And,

• Better error handing
• More user friendly

phasTER Release v.rc1.1

This is a release candidate. Please phasTER Wiki for details on installation, usage, output files and more.

• Updated settings file

phasTER Release rc.v1

This is first release candidate. Please see phasTER Wiki for details on installation, usage, output files and more.