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A shortcut script that executes all these functions on <input.fasta> and <reads.csfasta> is: 

Create a reference genome (note the -A 1 option means colorspace, use -A 0 for base space)

bfast fasta2brg -f <fastafile> and make a colorspace one too: bfast fasta2brg -f <fastafile> -A 1

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For something like bacteria, these are some reasonable masks. Note that both base space and color space indexes are created with these commands:

bfast index -f <fastafile> -m 111111111111111111 -w 12 -i 1

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bfast index -f <fastafile> -m 1111011101011111101111 -w 12 -i 5 -A 1

Use the indexes and reference genome to find CALs(Candidate Alignment Locations) (again, note -A 1 is colorspace)

bfast match -f <fastafile> -A 1 -r <fastq> > bfast.matches.fasta.reads.bmf

Align each CAL using a local alignment algorithm (again, note -A 1 is colorspace)

bfast localalign -f <fasta> -m bfast.matches.fasta.reads.bmf -A 1 > bfast.aligned.fasta.reads.baf

Filter/Prioritize alignments (again, note -A 1 is colorspace)

bfast postprocess -f <fasta> -i bfast.aligned.fasta.reads.baf -A 1 > bfast.reported.fasta.reads.sam

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