lrz.useful.software.md

sizecutter.py

统计N50,scaffold长度等信息

FALCON

experimental PacBio diploid assembler

quast.py

比较不同的assembly的质量，也可以统计assembly的信息
http://quast.bioinf.spbau.ru/manual.html

source activate /naslx/projects/pn69xe/di52zuy/ignite_tools_py3/
quast.py \
# specify reference assembly from NCBI
-r Cryptococcus_gattii_VGII_R265_WGS_GCA_002954075.1.fasta \
# specify output dir with -o
-o 10a_cgat_quast_canu_ont_ref \
# specify short reads
-1 cgat_hiseq_SRR1513844_1.trimmed.filteredq25.fastq.gz \
-2 cgat_hiseq_SRR1513844_2.trimmed.filteredq25.fastq.gz \
# pre-produced mapping bam file of illumina reads to the refercne genome assembly
--ref-bam Cryptococcus_gattii_VGII_R265_WGS_GCA_002954075.1_hisat2_mapped_sorted_SRR1513844.bam \
# pre-produced mapping bam file of illumina reads to our assembly of interest (canu ont pilon)
--bam cgat_canu_ont_assembly.contigs_hisat2_mapped_sorted_SRR1513844_pilon.bam \
# specify nanopore reads that will be mapped by quast
--nanopore cgat_ont_SRR6363418.porechopped_1kb.fastq.gz \
# specify nanopore reads that will be mapped by quast
--pacbio cgat_pacbio_SRR5891540_1kb.fastq.gz \
# number of threads/cores
-t 28 \
# specify the fasta of the genome of interest
cgat_canu_ont_assembly.contigs_pilon.fasta

下载包

module load nano

firefox

firefox *.pdf 直接从linux打开文件