Nanopore 分析常用软件目录
|软件名|功能|官方网址|
|----|----|----|
|bioconda|bioconda商店|http://bioconda.github.io/|
|sratoolkit|SRA数据管理|https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft|
|flappie|碱基识别|https://github.com/nanoporetech/flappie|
|albacore|碱基识别|https://github.com/Albacore/albacore|
|guppy|碱基识别|nanopore社区|
|MINKNOW|测序操控软件|nanopore社区|
|hdfview|查看fast5|https://www.hdfgroup.org/downloads/hdfview/|
|ont_fast5_api|拆分合并fast5|https://github.com/nanoporetech/ont_fast5_api|
|pomoxis|综合分析|https://github.com/nanoporetech/pomoxis|
|minion_qc|质控绘图|https://github.com/roblanf/minion_qc|
|Filtlong|过滤|https://github.com/rrwick/Filtlong|
|seqkit|序列处理工具包|https://bioinf.shenwei.me/seqkit/|
|nanopack|数据质控顾虑包|https://github.com/wdecoster/nanopack|
|NanoPlot|质控绘图|https://github.com/wdecoster/NanoPlot|
|Porechop|过滤|https://github.com/rrwick/Porechop|
|MaSuRCA|拼接|https://github.com/alekseyzimin/masurca|
|Tulip|拼接|https://github.com/Generade-nl/TULIP|
|spades|拼接|https://github.com/ablab/spades|
|canu|拼接|https://github.com/marbl/canu|
|NextDenovo|拼接|https://github.com/Nextomics/NextDenovo|
|RaGOO|参考引导|https://github.com/malonge/RaGOO|
|Unicycler|拼接|https://github.com/rrwick/Unicycler|
|MECAT|拼接|https://github.com/xiaochuanle/MECAT|
|NECAT|拼接|https://github.com/xiaochuanle/NECAT|
|miniasm|拼接|https://github.com/lh3/miniasm|
|WTDBG2|拼接|?https://github.com/ruanjue/wtdbg2|
|SMARTdenovo|拼接|https://github.com/ruanjue/smartdenovo|
|RA|拼接|https://github.com/rvaser/ra|
|gfatools|gfa文件处理|https://github.com/lh3/gfatools|
|medaka|纠错|https://github.com/nanoporetech/medaka|
|pilon|纠错|https://github.com/broadinstitute/pilon/wiki|
|racon|纠错|https://github.com/lbcb-sci/racon|
|NextPolish|纠错|https://github.com/Nextomics/NextPolish|
|quast|拼接评估|http://bioinf.spbau.ru/quast|
|busco|拼接评估|https://gitlab.com/ezlab/busco|
|bwa|短序列比对|https://github.com/lh3/bwa|
|samtools|sam格式处理|https://github.com/lh3/samtools|
|minimap2|比对|https://github.com/lh3/minimap2|
|NGMLR|比对|https://github.com/philres/ngmlr|
|last|比对|http://last.cbrc.jp/|
|GraphMap|比对|https://github.com/isovic/graphmap|
|MarginAlign|比对|https://github.com/benedictpaten/marginAlign|
|MUMMER|全局比对|http://mummer.sourceforge.net/|
|megan|物种鉴定|http://ab.inf.uni-tuebingen.de/software/megan6/download/|
|diamond|blast比对|https://github.com/bbuchfink/diamond|
|seqtk|序列处理工具|https://github.com/lh3/seqtk|
|taxonkit|物种分类鉴定|https://bioinf.shenwei.me/taxonkit/|
|Centrifuge|物种分类|https://github.com/DaehwanKimLab/centrifuge|
|Nanopolish|综合分析|https://github.com/nanoporetech/nanopolish|
|NanoSV|变异检测|https://github.com/mroosmalen/nanosv|
|Sniffles|变异检测|https://github.com/fritzsedlazeck/Sniffles|
|NanoVar|变异检测|https://github.com/benoukraflab/NanoVar|
|tombo|甲基化|https://github.com/nanoporetech/tombo|
|bcftools|vcf格式处理|https://github.com/samtools/bcftools|
|Truvari|变异检测|https://github.com/spiralgenetics/truvari/|
|Pinfish|异构体鉴别|https://github.com/nanoporetech/pinfish|
|pychopper|异构体鉴别|https://github.com/nanoporetech/pychopper|
|tablet|可视化|https://ics.hutton.ac.uk/tablet/|
|IGV|可视化|http://software.broadinstitute.org/software/igv/|