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Old 06-15-2011, 04:31 AM   #1
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Location: St. Louis, MO, USA

Join Date: Apr 2011
Posts: 124
Default BAMseek large file viewer - now with VCF and FASTQ support

Hi all,

I have recently made some updates to BAMseek - a large file reader for Next-Generation Sequencing files. Most notable is the support for viewing VCF and FASTQ files.

Currently you can open and view these Next-Gen file formats
- BAM/SAM alignment format - updated to support SAM spec v1.4 (specifically, the 'B'-type array tag)
- VCF variant call format : both uncompressed text files and BGZF-compressed files (which is how they are stored on the 1000 Genomes website, so no need to decompress the entire file before viewing it)
- FASTQ (reads+quality) format: with special recognition of the description lines in Illumina's CASAVA 1.8 fastq files.

The goal is to provide a convenient software for looking at the large and varied formats used in Next-Generation sequencing. These files usually cannot be easily viewed in common text editors (such as Word or TextEdit) because of their sizes or special format representations. BAMseek also provides useful tooltip pop-ups when you hover over a cell to provide more information about what you are looking at (see here for example of what the software looks like).

BAMseek is cross-platform, so should work on Windows/Mac/Linux. It uses the Picard library for working with BGZF files and is written in JAVA.

I am always looking to improve the software, so suggestions and bug reports are more than welcomed.

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Old 07-25-2011, 06:57 PM   #2
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Location: St. Louis, MO, USA

Join Date: Apr 2011
Posts: 124
Default Faster loading of large next-gen files

Hi all,

Upon request, BAMseek now creates an external index file for faster file loading. If the file has already been opened in BAMseek, then the index will be saved and the file will load faster the next time you open it.

Download is available here.

This could be useful for browsing large next-gen files you have on your desktop. It could also be used when hosting a large file on an FTP site - if you host the index file too, then the user could browse the file before downloading the entire thing.

BAMseek allows you to view the following file formats:
  • SFF
  • VCF (plain text and BGZF compressed)

Let me know if you have any questions or feedback.

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