#About BIC BIC - A bucket index correction based method for compression of genomic sequencing data.
https://github.com/rongjiewang/BIC.git
This is a software tool relying on GATB-CORE library, reads error correction tool Bloocoo and compression tool ORCOM.
The executable files of the tool is as follows:
* BIC_b - bucketing corrected reads into buckets.
* BIC_c - compressing each bucket with PPMd method.
BIC_b is run from the command prompt:
BIC_b <e|d> [options]
in one of the two modes:
e- encoding,d- decoding,
with mainly available options:
-in <file>- input file,-out <file>- output file,-kmer-size- size of a kmer [default '31'],-abundance-min- min abundance threshold for solid kmers [default 'auto'],-nb-cores- worker threads number, default:0,-verbose- verbose mode, default:false.
Encode (cluster) reads from input.fastq file.
BIC_b e -in input.fastq -out bucketFile
Decode reads from bucketFile bucket files and save the DNA reads to decode.dna file.
BIC_b d -in bucketFile -out decode.dna
BIC_c is run from the command prompt:
BIC_c <e|d> [options]
in one of the two modes:
e- encoding,d- decoding,
with available options:
- -i : BIC_c generated input files prefix
- -o : output files prefix
- -e : encode threshold value, default: 0 (0 - auto)
- -m : mismatch cost, default: 2
- -s : insert cost, default: 1
- -t : threads count, default: 8
- -v : verbose mode, default: false
Encode (compress) clustered reads from bucketFile bucket files and save the output to compressedFile archive files:
BIC_c e -ibucketFile -ocompressedFile
Decode reads from compressedFile archive files and save the DNA reads to decode.dna file.
BIC_c d -icompressedFile -odecode.dna