AI代码解释 python comb_coverage01.py-g An1.gaf-a An1-o An1Cov.tsv-rYpython comb_coverage01.py-gC24.gaf-aC24-o C24Cov.tsv-rNpython comb_coverage01.py-g Cvi.gaf-a Cvi-o CviCov.tsv-rNpython comb_coverage01.py-g Eri.gaf-a Eri-o EriCov.tsv-rNpython comb_coverage01.py-g Ler....
(2)chicken and zebra finch (long insert sanger)were significantly larger than those in other birds(short insert NGS), 所以认为测序方法对 identity gene 有影响,但不知道影响大不大,所以, evaluate: (1)测序深度对data的影响: 1.整体考查所有物种及其depth的关系: ascatter plot between the number of i...
Meanwhile, the relative abundance of a genome (relative coverage) is proportional to the relative fraction of total cells represented by the genome, rather than the relative fraction of total DNA represented by the genome. For example, a CPR genome with a relative abundance of 1% will constitute...
smudgeplot.py hetkmers -o smudgeplot_kmercounts/<kmc_db>.kmc_L"$L"_U"$U" < smudgeplot_kmc_db/<kmc_db>.kmc_L"$L"_U"$U".dump # Plot smudgeplot.py plot <kmc_db>._L"$L"_U"$U"_coverages.tsv 结果示意图如下,Smudgeplot给出了最有可能的kmer pair情况,从而来判定倍性 基因组大小估计...
设置参数k-mer length为第一步选择的k-mer长度值,这里是17;参数Read length为序列读长,一般为150;最后一个参数Max kmer coverage建议修改成更大的10000,以统计更多的k-mers。 结果显示预估的基因组大小,杂合度,重复率等信息。 5.1.2. GenomeScope2.0 网页版 —— 适用于多倍体物种 GenomeScope2.0 网页版也是类似...
(ref.2), could be mapped to the Weining assembly with an average sequence identity of 97.71% and a mean sequence coverage of 97.27%. Finally, 99.77% of the 2,769,537,530 Illumina paired-end reads generated in the present study could be mapped onto the assembly (Supplementary Table8). ...
Then, the sequencing depth, genome coverage, and other information of each sample were calculated based on the bam file. By using GATK 4.1.8.0 software to call SNPs, SNP mutations were detected based on the comparison results of clean reads in the reference genome. Then, the SNP standard ...
file of a related genome with Liftoff 1.6.1 [43]. With additional input data, the pipeline can detect ectopic mitochondrial and apicoplast sequences using BLAST 2.10.1 [34], and RNA-Seq read coverage using HISAT2 2.2.1 [44]. If the user provides proteome FASTA files of species that ...
A plot analysis of the fingerprinted clones versus the number of contigs (Fig. 2) indicated that the fingerprinted BACs (5.6× genome coverage) should provide a reasonable coverage of the whole genome of catfish. Although the calculated consensus band (CB) map distance was the same size as ...
We used short-read (100 bp), small-insert paired-end Illumina sequencing aiming to generate 20× coverage per individual. After quality control with trimmomatic, we mapped the qualified paired-end reads to the A. echinatior reference genome with bwa and removed duplicates with picard. We ...