Aligning fasta files

Question

[bioz]

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 ?

[Benn]

Try to use an aligner, bwa for instance.

[ATpoint]

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

[Benn]

OP wants bam file.

[ATpoint]

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

Suggesting an alternative.

[GenoMax]

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