科研、生信相关网站,持续更新。。。
2024/4/17
文献互助网站
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SCI-hub: https://sci-hub.se/
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高性能计算机High-performance computing (HPC)的使用
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上海交大超算平台用户手册: https://docs.hpc.sjtu.edu.cn/index.html
科研绘图
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ImageGP: http://www.bic.ac.cn/BIC/#/
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Matplotlib: https://matplotlib.org/ Visualization with Python
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seaborn: https://seaborn.pydata.org/
生信工具
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sentieon(Call SNP): https://support.sentieon.com/manual/#
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甘蔗数据库: http://sugarcane.zhangjisenlab.cn/sgd/html/index.html
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共线性工具Syri: https://github.com/schneebergerlab/syri syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.
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published plant genomes: https://www.plabipd.de/plant_genomes_pa.ep Phylogenetic relationships for flowering plants with genomes sequenced and published.
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多序列比对及进化受限位点计算MSA_pipeline: https://bitbucket.org/bucklerlab/msa_pipeline/src/master/ The msa_pipeline bundles existing tools to make multiple alignment of genomes easy.
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基因组下载
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NCBI: https://www.ncbi.nlm.nih.gov/ -
Ensembl: https://useast.ensembl.org -
EnsemblPlants: https://plants.ensembl.org/index.html -
Phytozome: https://phytozome-next.jgi.doe.gov/ -
UCSC Genome Browse: https://genome.ucsc.edu/ -
Published Plant Genomes: https://www.plabipd.de/plant_genomes_pa.ep -
国家基因组科学数据中心: https://ngdc.cncb.ac.cn/?lang=zh
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流程工具Snakemake: https://snakemake.readthedocs.io/en/stable/# The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
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容器工具Apptainer: https://github.com/apptainer/apptainer Singularity began as an open-source project in 2015, when a team of researchers at Lawrence Berkeley National Laboratory, led by Gregory Kurtzer, developed the initial version written in the C programming language and released it under the BSD license. In May 2020 Gregory Kurtzer left Sylabs but retained leadership of the Singularity open source project. In May 2021 Sylabs made a fork of the project and called it SingularityCE. In November 2021 the Singularity open source project joined the Linux Foundation and was renamed to Apptainer.
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有害突变SIFT4G: https://sift.bii.a-star.edu.sg/sift4g/ deleterious mutations analysis
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Softberry: http://www.softberry.com/
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比对工具bwa: https://bio-bwa.sourceforge.net/
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比对工具minimap2: https://lh3.github.io/minimap2/
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共线性工具jcvi: https://github.com/tanghaibao/jcvi/wiki/MCscan-%28Python-version%29
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加权共表达网络分析WGCNA
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Clustering using WGCNA: https://wikis.utexas.edu/display/bioiteam/Clustering+using+WGCNA -
WGCNA Gene Correlation Network Analysis: https://bioinformaticsworkbook.org/tutorials/wgcna.html#gsc.tab=0
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Bioinformatics Workbook: https://bioinformaticsworkbook.org/#gsc.tab=0
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