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- person_outline Zexuan Zhu
Publications for LW-FQZip
Optimal compressed representation of high throughput sequence data via light assembly
[…] ata set by either (i) assembling reads into long contigs, typically by a de Bruijn graph-based approach (e.g., Quip, Leon, k-Path, and KIC), or by (ii) aligning the reads to a reference genome (e.g., LW-FQZip); the reads are then encoded as simple pointers to the reference or the assembled contigs.Because both sequence mapping and assembly are computationally intensive tasks, all the above HTS com […]
I could compress the example fastq of 31M was to 8.6M. This is exactly the same size as if you would use gzip on this file. Using bzip2 the file size is reduced even further to 7.3M.
Additionally when I tried to compress my own fastq files (human) I got he error 'error genome file size'. After solving this issue in a hard coded way, I got a buffer overflow using the LWFQZip -c command.