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NEWS.md

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  • 0.14 (not released yet)
    • updated fermi2 to r193 for a fix of open end trimming
    • updated bwa to r1142 (post 0.7.15)
    • updated trimadap for one additional 3'-end PE adapter
    • updated hapdip to r56 for better filtering in the fermikit mode
    • updated htsbox to r327 (forgot if it has any effect on fermikit)
    • updated k8 to 0.2.2 as is required by more recent hapdip
    • the assembly components should almost the same as v0.13, except the fermi2 bugfix for good
  • 0.13
    • updated trimadap to r9 for trimming (not only masking)
    • updated hapdip to r36 for minor bug fixes
    • updated htsbox to r130 for a few minor changes and BAM sorting
    • dropped samtools dependency for BAM sorting (now by htsbox)
    • added test script (by Mike Lin)
    • The assembly components are identical to v0.12.
    • The calling components are also identical.
  • 0.12
    • updated htsbox to r302 for SV calling
    • updated hapdip to r19 for multi-sample filtering.
    • This is the first public release of fermi.kit.
  • 0.11
    • updated fermi2.pl to r188 for robustness (no method changes)
    • updated htsbox to r289 for quality binning and razip fix
    • The assembly is the same as v0.9
    • This version is not packaged.
  • 0.10
    • updated htsbox to r282 which fixed a bug in samview's PAF output.
    • updated bfc to r181 which fixes a potential out-of-order bug. This bug should almost never happen for normal use of bfc.
    • updated bwa to r1044 for the same bugfix as in bfc.
    • updated trimadap-mt to r8 for the same bug.
    • updated seqtk to r82. It comes with two new commands rename and gc, though they are not actually useful to the fermi.kit pipeline.
    • The assembly is the same as v0.9.
  • 0.9
    • updated fermi2.pl. It uses a new formula to automatically set -k.
    • updated htsbox to r281. No effective changes.
    • For 100bp reads, the assembly is the same as v0.8.
    • This version is used to produce the results in the manuscript.
  • 0.8
    • updated bfc to r177. r177 fixed a bug which causes segfault if the read length is close to 128, 256, 512bp, etc. The results should be the same (except the random effect).
    • fermi2.pl optionally skip error correction.
    • This version is used to assemble 261 SGDP samples.
  • 0.7
    • used to assemble SGDP public samples
    • used to assemble the CHM1-NA12878 pair v4