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Fix Fasta Headers for BUSCO

I aligned my paired end genome reads to a reference genome sequence using the BWA software, and it gave me a .sam file. I used samtools SAM to FASTA to convert the aligned reads to fasta file. I want to look at assembly statistics and also evaluate completeness with BUSCO. I received the following error:

The character "/" is present in the fasta header >A00600:204:HFMJ3DSX3:3:1101:3640:1125/1, which will crash Reader. Please clean the header of your input file.

when I do head -8 aligned.fasta this is what I get:

>A00600:204:HFMJ3DSX3:3:1101:3640:1125/1
TTTTATTTGAAATCACAAACCACTAACAACGATACAAAACGTCAATATATTCCCAAATTCGATGATTTTTTCTTCAAATCATGATGCGAGATTTTCTGGTATTTAGATCAATAAAATGCATATGAAAAGGTTGTTTCCAATACAAATGATC

>A00600:204:HFMJ3DSX3:3:1101:3640:1125/2
GGAATAGAGCGGTTTTACGTGTACATCTTCTTTCGGTAAAATAAACGGAATATCAAGTGAATTCTAATGAAAACACATTGATTTTGATCATTTGTATTGGAAACAACCTTTTCATATGCATTTTAATGATCTAAATACCAGGAAATCTCGC

>A00600:204:HFMJ3DSX3:3:1101:3658:1125/1
CCGAGTATTTTTGCCAGAATTGTTTTTCATATGTTGCCCAAACCCCCCTGCAGTTTTCCCAATATGGGAAATATCGCAATTCTGACTCGTGAGCGTTGTTTTGGAGCCGAATTGTGACTCCCTGCACATATTTGGAGTTTGAAATTCCGAG

>A00600:204:HFMJ3DSX3:3:1101:3658:1125/2
GGTTTGGGCAACATATGAAAAAAAATTCTGGCAAAATTCTCGGAATTTCAAACTCCAAATATGTGCAGGGAGTCACAATTCGGCTCCAAAACAACGCTCACGAGTCAGAATTGCGATATTTCCCATATTGGGAAAACTGCAGGGGGGTTTG

How can I clean up the fasta header so that BUSCO can run its analysis? Thank you for your help!

fasta bwa busco
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updated by GenoMax GenoMax • written by hpalk42 • hpalk42

1 answer

You could try replacing / with _:

$ sed 's/\//_/g' test.fa
>A00600:204:HFMJ3DSX3:3:1101:3640:1125_1
TTTTATTTGAAATCACAAACCACTAACAACGATACAAAACGTCAATATATTCCCAAATTCGATGATTTTTTCTTCAAATCATGATGCGAGATTTTCTGGTATTTAGATCAATAAAATGCATATGAAAAGGTTGTTTCCAATACAAATGATC
>A00600:204:HFMJ3DSX3:3:1101:3640:1125_2
GGAATAGAGCGGTTTTACGTGTACATCTTCTTTCGGTAAAATAAACGGAATATCAAGTGAATTCTAATGAAAACACATTGATTTTGATCATTTGTATTGGAAACAACCTTTTCATATGCATTTTAATGATCTAAATACCAGGAAATCTCGC
>A00600:204:HFMJ3DSX3:3:1101:3658:1125_1
CCGAGTATTTTTGCCAGAATTGTTTTTCATATGTTGCCCAAACCCCCCTGCAGTTTTCCCAATATGGGAAATATCGCAATTCTGACTCGTGAGCGTTGTTTTGGAGCCGAATTGTGACTCCCTGCACATATTTGGAGTTTGAAATTCCGAG
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written by GenoMax GenoMax

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