Additional file 1: of LW-FQZip 2: a parallelized reference-based compression of FASTQ files

This document provides the implementation details of LW-FQZip 2 and the detailed experimental results of each compared algorithm in the related comparison study. Algorithm 1. The main procedure of LW-FQZip 2. Algorithm 2. Compression with PPM prediction model and arithmetic coding. Table S1. The performance of LW-FQZip 2. Table S2. The performance of LW-FQZip 2 (−g). Table S3. The performance of LW-FQZip 1. Table S4. The performance of Quip (−a). Table S5. The performance of Quip (−r). Table S6. The performance of DSRC 2. Table S7. The performance of CRAM. Table S8. The performance of FQZcomp. Table S9. The performance of LFQC. Table S10. The performance of LEON. Table S11. The performance of SCALCE. Table S12. The performance of bzip 2. Table S13. The performance of gzip. Table S14. The average number of CPU cores used by the compared methods. Table S15. The compression ratios and time consumptions of LW-FQZip 2 w/o complementary palindrome mapping. Table S16. The memory usage of the LW-FQZip 2 w/o complementary palindrome mapping. Table S17. The version information of all compared methods. Table S18. The compression ratios of the compared methods on benchmark data provided by MPEG working group on genomic compression. Table S19. The performance of LW-FQZip 2 on benchmark data provided by MPEG working group on genomic compression. Table S20. The performance of LW-FQZip 2 (−g) on benchmark data provided by MPEG working group on genomic compression. Table S21. The compression ratios of LW-FQZip2 + LCP, LW-FQZip2 -g + LCP, SCALCE, and LW-FQZip 2 on seven representative data sets. Table S22. The comparison of compression speed of LW-FQZip 2 using SSD and HDD disk systems. Figure S1. The compression speeds of LW-FQZip 2 using different number of threads on five representative data sets. Figure S2. The framework of LW-FQZip 2 with LCP technique. (DOCX 229 kb