BAC-based validation of assemblies
- minimap2 >= 2.17
- R >= 3.5
- samtools >= 1.9
- bedtools >= 2.25
- GCC >= 4.8
These must all be available in your path.
All code developed by me is released into the public domain. Other code included in the repo may have different licenses, see the header present at the top of each file for details.
Clone the repo and compile the sam parsing code by running make. It should make a single binary named samToErrorRate. If that exists, the installation succeeded.
This pipeline assumes you have a file named bacs.fasta in the folder where you are running from your genome to validate. There are some BAC libraries in NCBI for several human genomes, for example CHM13, NA12878, and HG0733.
There is a single shell script, getStats.sh which takes one argument, a fasta file for your assembly. The script will align the bacs to your assembly, convert the sam to text, and report some statistics. Remove the sam and txt files to force the pipeline to re-map the bacs.
If you want to validate on a subset of BACs, e.g. ones coming from the unique regions of the genome or you have higher confidence in, create a file named goodBacs listing the IDs from the fasta file (up to the first space). The same getStats.sh script above will report stats only on this subset of BACs. You can do this after running the pipeline, the mappings won't be re-generated.
You can also adjust the default break length when mapping (which defaults to 2kb) to any other value by passing it as the second parameter (e.g. sh getStats.sh asm.fasta 5000 will use a break length of 5kb). This will map more BACs in single pieces but will decrease the identity since it will tolerage more noise in the alignment.
Example output for T2T v0.6 assembly
******************* BAC SUMMARY ******************
TOTAL : 341
BP : 51532183
************** Statistics for: chm13.draft_v0.6.fasta ****************
BACs closed: 280 (82.1114); BACs attempted: 310 %good = 90.3226; BASES 42501309 (82.4753)
Median: 99.98025
MedianQV: 37.04433
Mean: 99.80281
MeanQV: 27.05109
***** STATS IGNORING INDELS ********************
Median: 100
MedianQV: Inf
Mean: 99.96021
MeanQV: 34.00199