├── Manual ├── Admixture.md ├── Albacore.md ├── AnnotSV.md ├── Annovar.md ├── Assemblytics.md ├── BLAT.md ├── BUSCO.md ├── Canvas.md ├── DeepMod.md ├── DeepSignal.md ├── Eigenstrat.md ├── GATK.md ├── GATK_CNV.md ├── GATK_gvcf.md ├── GATK_variant.md ├── IGV-snapshot-automator.md ├── LAMSA.md ├── MAKE.md ├── MELT.md ├── MUMmer4.md ├── Manta.md ├── NanoSV.md ├── NanoSV_Sniffles_BND.md ├── NanoStat.md ├── NanoVar.md ├── PBS.md ├── PacBio.md ├── Pychopper.md ├── R_tips.md ├── RepeatMasker.md ├── RepeatModeler.md ├── Rstudio.md ├── STAR_RNA.md ├── SVIM_result.md ├── SVMU.md ├── Shimmer.md ├── SomaticSniper.md ├── Strelka.md ├── Varscan.md ├── alfred.md ├── annotation_interpretation.md ├── bcftools.md ├── bedtools.md ├── bioinformatic_general.md ├── blasr.md ├── blasr_smartiesv.md ├── busco.md ├── bwa.md ├── circos │ ├── circos.conf │ └── circos_config_file.md ├── cnvnator.md ├── cuteSV.md ├── dbNSFP2.9.3.txt ├── deepvariant.md ├── delly.md ├── denovoVariants.md ├── fastx_toolkit.md ├── freebayes.md ├── graphmap.md ├── gtftogenepred.md ├── igv_plotter.md ├── jupyter.md ├── last.md ├── linux.md ├── lollipops.md ├── long_reads.md ├── longshot.md ├── lordfast.md ├── mapper_evalution.md ├── medak.md ├── minialign.md ├── minimap2.md ├── mutect2.md ├── nanopolish.md ├── nanopore_kits.md ├── novoCaller.md ├── peregrine.md ├── picky.md ├── pinfish.md ├── pomoxis.md ├── prefetch.md ├── python_tips.md ├── quast.md ├── rHAT ├── rMETL.md ├── rice_pipeline.md ├── sambamba.md ├── samplot.md ├── snakemake.md ├── stringtie2.md ├── svim.md ├── svtools.md ├── svviz2.md ├── trimmomatic.md └── wtdbg2.md ├── Manual0 ├── 16S_history.md ├── 16S_rRNA_gene_database.md ├── Annovar.md ├── BaiduPCS-Go.md ├── Binsanity.md ├── CNCI.md ├── COG.md ├── COG_manual.md ├── CONCOCT.md ├── CRISPR.md ├── C_library.md ├── CallSNV_FAQ.md ├── Centrifuge.md ├── CheckM.md ├── DaPars.md ├── FREEC.md ├── GDC_TCGA.md ├── GO_compare.md ├── G_Statistics_for_BSA.md ├── GenomeTools.md ├── GraPhlAn.md ├── HTSeq.md ├── Infernal.md ├── KmerGenie.md ├── LTR_retriever.md ├── LTRharvest.md ├── MACS.md ├── MCScanX │ ├── MCScanX.md │ ├── data │ │ ├── circle.ctl │ │ ├── dual_synteny.ctl │ │ ├── os_sb.blast │ │ ├── os_sb.collinearity │ │ ├── os_sb.control │ │ └── os_sb.gff │ └── picture │ │ ├── os_sb.bar_plot.png │ │ ├── os_sb.circle.png │ │ ├── os_sb.dot.png │ │ ├── os_sb.dual.synteny.png │ │ └── syn_html.png ├── MECAT.md ├── MISA.md ├── MOCAT2.md ├── MetAML.md ├── MetaMLST.md ├── MetaPhlAn.md ├── Mutiple_sequence_alignment.md ├── Nanopore_QC.md ├── PICRUSt.md ├── PILER.md ├── PanPhlAn.md ├── Pfam.md ├── PhyloCSF.md ├── Prokka.md ├── RDA_analysis.md ├── README.md ├── RNA_variant.md ├── RSeQC.md ├── R_library.md ├── RepeatModeler.md ├── SILVA_error.md ├── SPAdes.md ├── SQLite.md ├── STAMP.md ├── STAMP │ ├── STAMP_interface.md │ └── pictures │ │ ├── analysis.png │ │ ├── data.png │ │ ├── group.png │ │ ├── legend.png │ │ ├── loading_data.png │ │ ├── result.png │ │ └── save.png ├── STAR.md ├── SURVIVOR.md ├── SignaIP.md ├── StrainPhlAn.md ├── TACO.md ├── Taxonomy_classification.md ├── Trim_adapters │ ├── Trim_adapters.md │ ├── picture │ │ ├── 1_raw.png │ │ ├── 2_SOAPnuke.png │ │ ├── 2_fastp.png │ │ ├── 3_SOAPnuke.png │ │ ├── 3_SOAPnuke_untrim.png │ │ ├── 3_fastp.png │ │ ├── R1_read.png │ │ ├── SOAPnuke.png │ │ ├── SOAPnuke_trim.png │ │ ├── compare.png │ │ ├── cutadapt.png │ │ ├── fastp.png │ │ ├── fastp_trim.png │ │ ├── raw_R1.png │ │ ├── raw_R2.png │ │ └── test_data.png │ └── test_data │ │ ├── trim_test.R1.fq │ │ ├── trim_test.R2.fq │ │ ├── trim_test_SOAPnuke.R1.fq │ │ ├── trim_test_SOAPnuke.R2.fq │ │ ├── trim_test_cutadapt.R1.fq │ │ ├── trim_test_cutadapt.R2.fq │ │ ├── trim_test_fastp.R1.fq │ │ └── trim_test_fastp.R2.fq ├── UID16S_report.md ├── UMI_TCR.md ├── Ubuntu.md ├── ViennaRNA.md ├── adonis_anosim.md ├── alignment_tools.md ├── anaconda.md ├── anvi.md ├── aspera.md ├── assembly_nanopore.md ├── assembly_tools.md ├── augustus.md ├── bamFlagReads.md ├── bamFlagReads.md.0 ├── bedtools.md ├── blast.md ├── blast_diamond.md ├── busco.md ├── canu.md ├── cazy_db.md ├── cd-hit.md ├── circos.md ├── cnvkit.md ├── database.md ├── deeptools.md ├── delly.md ├── denovoVariant │ ├── Triodenovo.md │ ├── denovoVariant.md │ └── denovogear.md ├── docker_bio.md ├── docker_general.md ├── docker_image.md ├── download_SRA_project.md ├── eggnog-mapper.md ├── ensemble_genome.md ├── falcon.md ├── gaf_format.md ├── gene_annotation.md ├── gene_ontology.md ├── git_manual.md ├── greengenes.md ├── hexo.md ├── hexo_markdown_math.md ├── hmmer.md ├── hmmsearch.md ├── humann2.md ├── idmapping_db.md ├── japsa.md ├── jcvi.md ├── jellyfish.md ├── jupyter.md ├── jvarkit.md ├── kaiju_krona.md ├── kegg_db.md ├── kneaddata.md ├── lastz.md ├── linux_general.md ├── lordfast.md ├── mafft.md ├── manta.md ├── maxbin.md ├── megahit.md ├── merge_PE_fastq.md ├── metabat.md ├── metaphyler.md ├── metaquast.md ├── minimap2.md ├── mosdepth.md ├── mothur.md ├── mummer.md ├── mysql.md ├── mysql_ZFC.md ├── nanopack.md ├── ngmlr.md ├── orthomcl.md ├── parallel.md ├── pblat.md ├── pbs.md ├── perl_general.md ├── pigz.md ├── prefetch.md ├── prodigal.md ├── protein_database.md ├── pynast_FastTree.md ├── python_code.md ├── qiime_workflow.md ├── quast.md ├── repeatscout.md ├── reports.md ├── rmats.md ├── salmon.md ├── samtools.md ├── sentieon.md ├── seq_tools.md ├── seqkit_for_FREEC.md ├── sniffles.md ├── snpEff.md ├── soapfuse.md ├── sourmash.md ├── sphinx.md ├── structural_variation.md ├── tRNA.md ├── taxonomy.md ├── usearch.md ├── variant_calling.md ├── vcfstats.md ├── vcftools.md ├── vsearch.md └── xlsx2csv.md ├── README.md ├── genome.md ├── gist ├── CommonLongestString.py ├── ExtractFastaFromList.py ├── FisherExactTest.py ├── RegionGenes.py ├── cut_fastq.py ├── delete_file_based_dir.py ├── fasta2fastq.pl ├── fasta_low_base_ratio.py ├── get_uniq_blast_record.py ├── plot_function.py ├── plot_function.r └── sparse_bed_for_gene.py ├── graphics ├── ManhattanPlot.r ├── qqPlot.r └── venn_3groups_plot.r ├── omictools.md ├── scripts ├── Annotation2GeneGO │ └── Annotation2GeneGO.py ├── Bnapus_GO │ ├── Bnapus_GeneGO.md │ ├── createBnapusGOdb.py │ └── data │ │ ├── Brassica_napus.annotation_v5.gff3 │ │ ├── Brassica_napus_GO │ │ └── term.txt ├── ChangeSampleName │ ├── ChangeSampleName.py │ └── test │ │ ├── LSS0-ZW-4.R1.fq.gz │ │ └── LSS3-CR-3.R1.fq.gz ├── ChrVariationDistribution │ ├── ChrVariationDistribution.py │ ├── Track1_snp_distribution.txt │ └── Track1_snp_test.txt ├── CombineDirFasta │ └── CombineDirFasta.py ├── CommonSpecificRegions │ ├── CommonSpecificRegions.py │ ├── KY131___WCY58_snp_index_number_win_sliding_sig_cont.xls │ └── WCY1___WCY58_snp_index_number_win_sliding_sig_cont.xls ├── DownloadGenomes.py ├── FastxSeqLen │ ├── FastxSeqLen.py │ ├── HistPlot.R │ └── SeqLensDistribute.py ├── GetTargetRecord │ ├── GetTargetRecord.py │ ├── gene │ └── gene_coverage_test.txt ├── OTUCategoryRatio │ ├── CategoryRatio.py │ ├── otu_table.txt │ └── otu_table_category.txt ├── Phylogenetic │ ├── Acinetobacter.fasta │ ├── Acinetobacter.mega.meg │ ├── Acinetobacter_nei_join.tree.mtsx │ ├── Acinetobacter_nei_join.tree.tif │ ├── ExtractSpeciesSeq.py │ └── README.txt ├── Primer3Result │ ├── C100_primer_report.html │ ├── C100_primer_report.xls │ └── Primer3Result.py ├── RDA │ ├── RDACorModify.R │ ├── Samples_taxonomy_species_test.txt │ └── sample_factors_test.txt ├── Scatter_plot.R ├── SeqCountLogo │ ├── SeqCountLogo.py │ └── seq_logo.png ├── SplitGenome2Chrs │ └── SplitGenome2Chrs.py ├── SubSample.py ├── TargetColumns │ ├── TargetColumns.py │ └── test ├── TargetTaxaGenes │ ├── TargetTaxaGenes.py │ ├── representive.faa.annotation_test.xls │ └── representive.faa.diamond_taxonomy_species_test.txt ├── combineDirfiles │ ├── CombineDirFiles.py │ └── DirfastqStats.py ├── downloadNCBISRA.py ├── flowerVenn │ ├── C186_group_special_OTUs.xls │ └── flowerVennPlot.R ├── freeNode.py ├── genus2taxonomy │ ├── genus2taxonomy.py │ ├── genus2taxonomyParallel.py │ ├── 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