flye
, pilon
Program: flye-kit: long reads assembly with Flye and Pilon.
Version: 0.0.1
Contact: ZHANG LEI <zhanglei@logictek.cn>
Usage: flye-kit [options]
Options:
-1 STR FASTQ file of first short reads in each pair. (required)
-2 STR FASTQ file of second short reads in each pair. (required)
-l STR FASTQ or FASTA file of long reads. (required)
-q STR long reads quality: pacbio-raw | pacbio-corr | pacbio-hifi |
nano-raw | nano-corr | nano-hq (required)
-n STR strain name for sequence label. (required)
-g STR estimated genome size (for example, 5m or 2.6g), (required)
-o STR Output directory (required)
-p STR Other Flye parametes. default: [""]
-t INT CPU number, default: [40]
-r INT rounds for pilon polish, default: [2]
CMD:
flye-kit -1 illumina/L_1.clean.fq.gz -2 illumina/L_2.clean.fq.gz -l nanopre/L.fq.gz -q nano-raw -n L -g 13m -o L