| 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/ |
