- 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
renameandgc, 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