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. solid2fastq.pl 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 aln.cs.map ref.csbfa out.bfq 2>aln.log : this maps the reads to the reference- the mapping is done in colorspace.

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

8. maq assemble out.cns ref.bfa aln.nt.map : 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 aln.nt.map > aln.nt.info

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