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.
Thanks!
BAMseek
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.
Thanks!
BAMseek
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