Ngs RestoreUnoptimizedBamFiles.pdf

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Restore Unoptimized BAM Files

Omicsoft implemented a tool to compress BAM files by compressing the quality to binary (low/high instead of numeric) and by changing read names to integers (read more details CompressBam). This utility is used to restore the full BAM files from compressed BAM (this process requires original fastq files). There is no way to restore full BAM if compressed from BAM tools (also called post-alignment comrpessed bam files).

RestoreUnoptimizedBamFiles 1.jpg



The "Input format" include FASTQ, FASTA, QSEC, SFF or AUTO (AUTO allows the use of any combination of the listed file types).

The Input files must be the original raw read files used to generate the compressed BAM files. If adapter stripping was used when generating the compressed BAM files, users must provide the adapter stripped fastq files here.


  • BAM folder - Browse for the directory where compressed BAM file is saved.
  • Output folder - Browser for the directory where users want to output the restored/uncompressed BAM file.
  • Reads are paired (files will be automatically paired) - The user can choose whether this is a paired end sequencing analysis, and if so, the reads will automatically be paired using a numbering system (_1, _2 or .1, .2).
  • Job number - Specifies the number of jobs running in parallel.
  • Zip format - Specify if the input files are zipped.