fu-orf

Extraction of ORFs from raw reads datasets (and other sequence files). Open reading frames are defined as a stretch of aminoacids not interrupted by stop codons: this program does not perform any gene finding procedure and merely extracts ORFs (under the assumption that, running on raw reads, fragments are expected).

A major update was introduced with version 1.8.4, with improved reporting (strand and reding frame in the output), improved tests and --scan-reverse option (previously enabled by default).

fu-orf 

Extract ORFs from Paired-End reads.

  Usage: 
  fu-orf [options] <InputFile>  
  fu-orf [options] -1 File_R1.fq
  fu-orf [options] -1 File_R1.fq -2 File_R2.fq
  fu-orf --help | --codes
  
  Input files:
    -1, --R1 FILE           First paired end file
    -2, --R2 FILE           Second paired end file

  ORF Finding and Output options:
    -m, --min-size INT      Minimum ORF size (aa) [default: 25]
    -p, --prefix STRING     Rename reads using this prefix
    -r, --scan-reverse      Also scan reverse complemented sequences
    -c, --code INT          NCBI Genetic code to use [default: 1]
    -l, --min-read-len INT  Minimum read length to process [default: 25]
  
  Paired-end optoins:
    -j, --join              Attempt Paired-End joining
    --min-overlap INT       Minimum PE overlap [default: 12]
    --max-overlap INT       Maximum PE overlap [default: 200]
    --min-identity FLOAT    Minimum sequence identity in overlap [default: 0.80]
  
  Other options:
    --codes                 Print NCBI genetic codes and exit
    --pool-size INT         Size of the sequences array to be processed
                            by each working thread [default: 250]
    --verbose               Print verbose log
    --debug                 Print debug log  
    --help                  Show help

Example usage

Single input file (FASTA or FASTQ):

fu-orf --min-size 500 data/orf.fa.gz  

Paired-end Illumina reads:

fu-orf --min-size 29  -1 data/illumina_1.fq.gz -2 data/illumina_2.fq.gz 

will produce a FASTA output reporting, as comment, the frame and the total ORFs printed for each sequence:

>filt.1_1 frame=+0 tot=5
RNLIILKMDFFFENFALVGLLYGACQRLNSTKFYLMSTDYLIVKTFNNGSLGSRIDEERS
>filt.1_2 frame=+2 tot=5
WSFRGSKSRNKVSVGEPAEGSLKKFNNFENGFFF
>filt.1_3 frame=+2 tot=5
KLCFGRPSIWGLPEVKLNQILFNVNRLFNSQNFQQRISWFSHR
>filt.1_4 frame=-1 tot=5
NLVEFNLWQAPYRRPTKAKFSKKKSIFKIIKFL
>filt.1_5 frame=-2 tot=5
LLNNRLTLNKIWLSLTSGRPHIEGLPKQSFQKKNPFSKLLNFFNDPSAGSPTETLLRLLLPLNDQ
>filt.2_1 frame=+0 tot=5
TYNQFFINLSHQIITNSQNFQQRISWFSHRNA
>filt.2_2 frame=+1 tot=5
NKLALAVGPACRQRSKLTTNFLSTCHTRLLLIVKTFNNGSLGSRIETQ
>filt.2_3 frame=+2 tot=5
WSFRGSKSRNKVSVGEPAEGSLLICLIAPHVFFFETNLLWRWAQPAARGLNLQPIFYQLVTPDYY
>filt.2_4 frame=-1 tot=5
KIGCKFRPLAAGWAHRQSKFVSKKNTCGAIKQISNDPSAGSPTETLLRLLLPLNDQ
>filt.2_5 frame=-2 tot=5
QVDKKLVVSLDLWRQAGPTAKASLFQRKTHVVQLSKSVMILPQVHLRKPCYDFYFL

Genetic codes

Genetic codes can be changed using NCBI Genetic Codes.

Type fu-orf --codes to print the following list.

• 1: The Standard Code
• 2: The Vertebrate Mitochondrial Code
• 3: The Yeast Mitochondrial Code
• 4: The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
• 5: The Invertebrate Mitochondrial Code
• 6: The Ciliate, Dasycladacean and Hexamita Nuclear Code
• 9: The Echinoderm and Flatworm Mitochondrial Code
• 10: The Euplotid Nuclear Code
• 11: The Bacterial, Archaeal and Plant Plastid Code
• 12: The Alternative Yeast Nuclear Code
• 13: The Ascidian Mitochondrial Code
• 14: The Alternative Flatworm Mitochondrial Code
• 16: Chlorophycean Mitochondrial Code
• 21: Trematode Mitochondrial Code
• 22: Scenedesmus obliquus Mitochondrial Code
• 23: Thraustochytrium Mitochondrial Code
• 24: Rhabdopleuridae Mitochondrial Code
• 25: Candidate Division SR1 and Gracilibacteria Code
• 26: Pachysolen tannophilus Nuclear Code
• 27: Karyorelict Nuclear Code
• 28: Condylostoma Nuclear Code
• 29: Mesodinium Nuclear Code
• 30: Peritrich Nuclear Code
• 31: Blastocrithidia Nuclear Code
• 33: Cephalodiscidae Mitochondrial UAA-Tyr Code