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Aligning fasta files
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15 months ago
bioz • 10

Hello stars, I have two fasta files, one is from Sanger sequencing machine out put and other is reference file. I want to align these fasta files and need out put in SAM/BAM format. Any idea, solution ?

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Try to use an aligner, bwa for instance.

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Sounds like a bit of an overkill for a single fasta sequence. Why not a pairwise alignment with EMBOSS-Needle?

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OP wants bam file.

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Sounds like a bit of an overkill for a single fasta sequence

Suggesting an alternative.

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You can use bbmap.sh from BBMap suite. Something like this:

bbmap.sh -Xmx10g in=sanger.fa  ref=ref.fa out=align.sam

if you have samtools available in your $PATH then you can directly output a BAM file.

bbmap.sh -Xmx10g in=sanger.fa  ref=ref.fa out=align.bam
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