MR_test Files

MR_test: Performs a series of Metarmorphic Relations to FastQ files and runs a short-read alignment software (choices of BWA, Bowtie or Bowtie2)

It requires installation of samtools, bwa, bowtie and bowtie2.

Usage: ./MR_TEST -program -MR[0-9]  [-S or -I]  (ref or ref.fa)  read1.fastq.gz  read2.fastq.gz  outputName
Options: -program -bwaS  BWA with single read
                              -bwaP  BWA with paired-end reads
                              -btS    Bowtie with single-end reads
                              -btP    Bowtie with paired-end reads
                              -bt2S Bowtie2 with single-end reads 
                              -bt2P   Bowtie2
              -MR[0-9] -MR0 Test All MR properties
                             -MR1 Randomly shuffle the reads in the fastq file
                             -MR2 Permute the sequence in the fastq file (A->T,T->A,G->C,C->G)
                             -MR3 Duplicate input sequence and added back to the input file
                             -MR4 Halves the input sequence
                             -MR5 Extend each read by a certain number of nucleotide to the 3' or 5' end of the read with high quality, based on the reference genome
                             -MR6 Remap all unmappable reads against the genome again
                             -MR7 Remap all mappable reads against the genome again (properly paired - only for paired end)
                             -MR8 Increase the quality score for all mapped sequences
                             -MR9 Correct the error in the reads
              -S Sanger fastq Format
              -I Illumina fastq Format