$ hifiasm Usage: hifiasm [options] <in_1.fq> <in_2.fq> <...> Options: Input/Output: -o STR prefix of output files [hifiasm.asm] -i ignore saved read correction and overlaps -t INT number of threads [1] -z INT length of adapters that should be removed [0] --version show version number Overlap/Error correction: -k INT k-mer length (must be <64) [51] -w INT minimizer window size [51] -f INT number of bits for bloom filter; 0 to disable [37] -D FLOAT drop k-mers occurring >FLOAT*coverage times [5.0] -N INT consider up to max(-D*coverage,-N) overlaps for each oriented read [100] -r INT round of correction [3] Assembly: -a INT round of assembly cleaning [4] -m INT pop bubbles of <INT in size in contig graphs [10000000] -p INT pop bubbles of <INT in size in unitig graphs [100000] -n INT remove tip unitigs composed of <=INT reads [3] -x FLOAT max overlap drop ratio [0.8] -y FLOAT min overlap drop ratio [0.2] -u disable post join contigs step which may improve N50 --lowQ INT output contig regions with >=INT% inconsistency in BED format; 0 to disable [70] Trio-partition: -1 FILE hap1/paternal k-mer dump generated by "yak count" [] -2 FILE hap2/maternal k-mer dump generated by "yak count" [] -c INT lower bound of the binned k-mer's frequency [2] -d INT upper bound of the binned k-mer's frequency [5] -3 FILE list of hap1/paternal read names [] -4 FILE list of hap2/maternal read names [] Purge-dups: -l INT purge level. 0: no purging; 1: light; 2: aggressive [0 for trio; 2 for unzip] -s FLOAT similarity threshold for duplicate haplotigs [0.75] -O INT min number of overlapped reads for duplicate haplotigs [1] --purge-cov INT coverage upper bound of Purge-dups [auto] --high-het enable this mode for high heterozygosity sample [experimental, not stable] Example: ./hifiasm -o NA12878.asm -t 32 NA12878.fq.gz See `man ./hifiasm.1' for detailed description of these command-line options.
微信
支付宝
