Genewiz gave me bam files instead of fasta files- can I convert bam to fasta to have a genome assembly?

Question

[kristina.mahan]

I had three bacterial genomes sequenced and Genewiz gave me fastq sequencing reads and bam files. I want the assembly fasta file- can I generate it myself using samtools bam to fasta? This sequencing project was done last year and it is unlikely that Genewiz has this data.

[ATpoint]

Did you ask them to create an assembly? If not then you must assemble it yourself, for this please google for tutorials on genome assembly. The raw sequencing data are just the genome chopped into pieces and sequenced, this is how NGS works.

[swbarnes2]

I'm not quite sure what you want. You want to make a de novo assembly based on your reads? You can do that with the fastq. You want to recreate the genome that the reads were aligned to to make the bam? I don't think you can do that easily.

Answer 1

[colindaven]

Use the FASTQ files with the program Flye to create a FASTA assembly. https://github.com/fenderglass/Flye

Alternatively, try SPADES.

Both are installable via miniconda I believe.