软件安装服务（更新）

计算中心安装了丰富的软件资源，为了用户在软件版本间更好的使用体验，计算中心采用module环境管理软件，可随时加载和卸载，不同版本间自由切换，这样做可以使得内核的大小和通信量都达到最小，计算中心还支持并行计算，可以把多个结点上的磁盘组织成为一个大的存储系统，提供更大的存储容量和聚集的I/O带宽，并随系统规模的扩大而扩展，在多种存储环境下发挥着重要的作用，尤其是集群结构的高性能计算领域，还提供并行程序设计咨询、并行程序调试、串并行程序性能优化等服务，帮助用户解决软件问题，优化程序设计，显著改善程序性能，更快更优地获得计算结果。

已安装的软件列表：《bwa, cactus, cuda10.0/10.1/9.1, cutadapt/2.8, dock6, dsq, CNVnator, GATK3/4 , ImageJ/2.0.0, MATLAB/R2018b, OPtiType/1.3.2., R3.5/3.6/, RSEM, STAR/2.5.3 ,anaconda3, SRAtoolkit, augustus, bcftools, blast, bowtie, intel-compiler/2018|2019, kobas, Kyoto, openmpi, openbabel,perl, openblas/0.3.7, samtools/1.9, tophat/1.3.2|2.1.0, subread, python3,hdf5/1.10.6,sambamba/0.7., samblaster/0.1.24, platypus , scanorama/1.4 ,hisat2, fastp, ffmpeg, NextDenovo，cudamat，htseq/0.11.2 ,htslib/1.9 ,fsl/6.3.0 , jellyfish/2.3.0,bcftools/1.9,bedToGenePred,bedtools/2.29.2, MaSuRCA，trinity，HiC-Pro/2.11.1, rstudio, masurca/3.3.5,TensorRT/6.0.1.5, vaa3d/2.921, apbs/1.5, blasr/5.3.3, bustools/0.39.3, centrifuge/1.0.4, clustalw2, cufflinks/2.2.1, delly/0.8.2 , emboss/6.6.0, fastqc/0.11.7, fftw/3.3.8 , flappie/2.1.0, g_mmpbsa/5.1.2, gdc/1.4.0, genePredToBed, genePredToGtf, genomestrip/2.00.1949, genompy/0.5.2, gff3ToGenePred, gmap, gnuplot/5.2.8 , gromacs-cpu/2020,201905 , gromacs-gpu/2020, gtfToGenePred , guppy/3.4.4, hyphy/2.5.2，kallisto/0.46.1，kraken/2.0.8，macs2/2.2.6，manta/1.6.0，minimap2/2.17，mummer/4.0.0，nanopack，，openblas/0.3.7，popins/popins，salmon/0.13.1，speedseq/0.1.2，sratoolkit/2.9.6，,trf/4.09，trim_galore/0.6.5，wham/1.7.0，homer，seqtk, plink, vcftools, svtk, svtools, sratoolkit, pycoQC, blat, bismark,  bs-seeker2, stap, smrtanalysis, gdc, PEGASAS, circis, lastz, RepeatMasker, GenomeAlignmentTools, kentUtils, bioawk, magma, bioawk, multiqc , seqkit, stringtie, velvet, sickle, gffcompare, featurecounts, mageck，gffread，cpat，pfam-scan，Hermite,admixture , FastTree, FigTree，phylowgs，bamtools，deeptools，gsl，lima ,pbccs ,isoseq , MATLAB/R2019a，cupcak，lr2rmats，rMATS, DeepMod, albacore,nanopolish, hdfview, deepsignal，REDItools2，genblasta，tablet，openbabel，ont_fast5_api，graphmap，canu ,pilon, NanoFilt, Trimmomatic, RAGOO, PyMOL. Pycharm,fast5-to-fastq, RagTag, raxml-ng, phydl，ensembl-vep，Graphtyper2，KING，MUSCE，dnaml，Snphylo，EIGENSOFT， PBSuite，VG，BreakDancer，svimmer，VaPoR ，GRIDSS，Lumpy，Manta，Wham，SVseq2，SoftSV，BayesTyper，toil-vg，iqtree,  seqwish,primer3, physpetools,  pySCENIC,HAL ，phast，AFNI , Freesurfer ,FSL, Mricron, Diffusion,  Trackvis, Mrtrix，Pytorch, FreeCAD,HIRise, Meraculous, Falcon, LACHESIS,  diamond , Rhapsody,genewise，SolexaQA，deepmind,ALLHIC, gdal , AnnoLnc, 3d-dna, sratoolkit, Fmripre, ANTs, C3D, ICA-AROMA ,bids-validator, connectome-workbench , Nipype ,juicer, datalad，raxml,  smcpp , psmc, braker , prothint, VCF-kit, busco ,metaeuk, piodigal, hmmer, sepp ,SV-plaudit , NGSadmix，pyclone, flye，SNPEff, spark，PSITE，edirect，MS,expect， RevTrans，SPOT-RNA，xcp_abcd，acpype，xcpEngine，jo，hcp2bids,ProteinGAN, QSIprep, datamash, nanocompore, rosetta,cuda/10.1, RepeatModeler, megax, RepeatScout,TRF, GeneMark-ES/ET, fastclone_guanlab, hexedit，mugsy，jvarkit，czplib，gvst,fastx, paup, Nextstrain，tabix，Sequenza,AlphaFold，juicebox，Sailor，redundans，wtdbg2，RoseTTAFold，pipelines, ClipKIT，genomescope，jellyfish，trimal，pyclone-vi，quast，hifiasm，bandage，PSiTE，snakemake，nextflow，simpleelastix，treebest, Porechop, bedGraphToBigWig, Haploview，Autodock4，denovogear，forestdnm，LiteCall，g-phocs，r-sctransform，dv_trio/1.0.0，famsep/1.0.3，gsutil/5.6，vt/0.57，rstudio/1.1.463，R/4.1.0，denovogear/dev，ffmpeg/4.2.1_gpu，varscan/2.3.9，stereopy/0.2.2，velocyto/0.17.17，bam-readcount/1.0.1，rclone/1.58.0，julia/1.7.2，salmon 1.8.0，guppy 6.1.2/cpu、guppy 6.1.2/gpu,napari/0.4.15，cell2location/0.1、SpaGCN/1.2.5,opencv/3.4.1, openpose/1.4.0, caffe/1.0, protobuf/3.13.0, google-glog/0.6.0, google-gflags/2.2.2, mtag/0.9.0, gwas/0.21, deeplabcut/2.2.1.1, rtg-tools/3.12.1, ldsc/1.0.0, velocyto/0.17.17, dynamo/0.7.17, clairvoyante，stack，alphafold/2.2.2，bamdst，spateo，anndata，scanpy,spateo, hicexplorer, Bullseye，inferCNV，fastcsr，DPAM，dnbc4tools，MNI_N3，copykat，BioImageIT，pySCENIC，CCP4，phenix，chimera，Relion，Cryosparc，ZDOCK，fusion，LOGODetect，micro-manager, exonerate, zrank, xvfb-ru, igv-snapshot-automator, Lightgbm，pbmm2，ReditoolsV1，MeRIPseqPipe，depict，scdrs，rpy2，hap.py，VarBen，IsoSeq3，LongQC，purge_haplotigs,mitoz,alphafold/2.3.0,Margin, medaka,PEPPER,detalad,vaa3d_tools, stitching-spark,GenomeTools,gemoma, SNAP,EVM (Evidence Moduler), mmseqs,miropeats, smashpp,PASA,cDNA_Cupcake TransDecoder, truvari, svviz, MitoFinder,LTR_FINDER,LTR_retriever, nvidia-cuda-runtime, antismash,sqanti3, TOSICA, MAKER, swan_vis》

联系方式：

王彦敏

计算中心

wangyanmin@cibr.ac.cn