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Using Maq 0.6.6 for colorspace alignment:

Note: Compatibility issues with Maq 0.7.1 and Maqview 0.2.3 have been experienced. So, use Maq 0.6.6 and maqview 0.2.3 together.

With colorspace reads file readsF3.csfasta and readsF3_QV.qual and reference file ref.fasta

1. reads out : this converts the csfasta and quality file into mock based fastq file called out.fastq

2. maq fastq2bfq out.fastq out.bfq : this converts the fastq file into binary format

3. maq fasta2csfa ref.fasta > ref.csfa  : this converts the reference file into mock based reference

4. maq fasta2bfa ref.csfa > ref.csbfa : this converts the mock based reference file into binary format

5. maq fasta2bfa ref.fasta > ref.bfa  : this converts the original reference file into binary format (for use in step 7 and 8)

6. maq map -c ref.csbfa out.bfq 2>aln.log : this maps the reads to the reference- the mapping is done in colorspace.

7. maq csmap2nt ref.bfa : this converts the color alignment to nucleotide alignment ( After this step, the color reference file and color alignment will not need to be used.

8. maq assemble out.cns ref.bfa : this creates a consensus sequence (out.cns) from the mapping results

Additionally, to convert any mapping result file (.map) to a readable tab delimited file, use:

maq mapview >

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