nanopore 分析常用软件目录

ONT nanopore常用软件清单

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/