sorted_tools2

* Abruijn (https://github.com/fenderglass/ABruijn)


* [adapterremoval](https://github.com/MikkelSchubert/adapterremoval): rapid adapter trimming, identification, and read merging

* [albacore](https://github.com/dvera/albacore)
* [algorithms](https://github.com/keon/algorithms): Minimal examples of data structures and algorithms in Python

* [allbiotc2](https://github.com/ALLBio/allbiotc2): Benchmark pipeline for Structural Variation analyses, funded by the ALLBio

* [ariba](https://github.com/sanger-pathogens/ariba): Antimicrobial Resistance Identification By Assembly
* [arriba](https://github.com/suhrig/arriba): Fast and accurate gene fusion detection from RNA-Seq data


* [awesome-10x-genomics](https://github.com/johandahlberg/awesome-10x-genomics): List of tools and resources related to the 10x Genomics GEMCode/Chromium system
* [awesome-nlp](https://github.com/keon/awesome-nlp): A curated list of resources dedicated to Natural Language Processing (NLP)
BackSPIN: https://github.com/linnarsson-lab/BackSPIN
* [bamkit](https://github.com/hall-lab/bamkit): Tools for common BAM file manipulations
* [bam-readcount](https://github.com/genome/bam-readcount): count DNA sequence reads in BAM files
* bamtools (https://github.com/pezmaster31/bamtools)

* [bcbio_validation_workflows](https://github.com/bcbio/bcbio_validation_workflows): A community menagarie of automated variant validations using bcbio and the Common Workflow Language
* [bioawk](https://github.com/lh3/bioawk): BWK awk modified for biological data
* [biobambam2](https://github.com/gt1/biobambam2): Tools for early stage alignment file processing

* [Blight](https://github.com/Malfoy/Blight): De Bruijn graph representation in low memory
Bowtie2, http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
* [bsseq](https://github.com/hansenlab/bsseq): Devel repository for bsseq
* bwa (https://github.com/lh3/bwa)
* [bwa](https://github.com/lh3/bwa): Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
* [bxtools](https://github.com/walaj/bxtools): Tools for analyzing 10X Genomics data
* Canu (https://github.com/marbl/canu)
* [capsim](https://github.com/mdcao/capsim): Simulation of capture sequencing
* [CellBench_data](https://github.com/LuyiTian/CellBench_data): This contains the dataset for comparing scRNA-seq analysis methods
* [cgpBattenberg](https://github.com/cancerit/cgpBattenberg): Battenberg algorithm and associated implementation script
* [CharGer](https://github.com/ding-lab/CharGer): Characterization of Germline variants
China Rice Data Center, http://www.ricedata.cn/gene/

CIDR: https://github.com/VCCRI/CIDR

* [Clairvoyante](https://github.com/aquaskyline/Clairvoyante): a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
* [cloudbiolinux](https://github.com/chapmanb/cloudbiolinux): configure virtual (or real) machines with tools for biological analyses


* [Compatible Software](https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software)

* [Complete-Striped-Smith-Waterman-Library](https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library): An SIMD Smith-Waterman C/C++/Python/Java Library for Use in Genomic Applications

-c /opt/albacore/r94_450bps_linear.cfg \

* [Coursera-ML-AndrewNg-Notes](https://github.com/fengdu78/Coursera-ML-AndrewNg-Notes): 吴恩达老师的机器学习课程个人笔记
* [CRISPResso2](https://github.com/pinellolab/CRISPResso2): Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
* [cyvcf2](https://github.com/brentp/cyvcf2): fast VCF and BCF processing	
* [CyVCF document](http://pyvcf.readthedocs.io/en/latest/)
* [CyVCF](https://github.com/arq5x/cyvcf): A fast Python library for VCF files leveraging Cython for speed.
* [Data Processing Pipelines](https://www.encodeproject.org/pipelines/)
* [DBG2OLC](https://github.com/yechengxi/DBG2OLC)
* [dbvar](https://github.com/ncbi/dbvar)









* [dockerfiles](https://github.com/jessfraz/dockerfiles): Various Dockerfiles I use on the desktop and on servers
* [docker](https://github.com/chef-cookbooks/docker): Chef Cookbook for Docker



EMBOSS, http://emboss.sourceforge.net

* [EnrichedHeatmap](https://github.com/jokergoo/EnrichedHeatmap): make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions
* [eXpert Model](https://github.com/mdcao/xm): The expert model compression model
* Falcon-integrate (https://github.com/PacificBiosciences/FALCON-integrate)


* [fastahack](https://github.com/ekg/fastahack/): utilities for indexing and sequence extraction from FASTA files
* [fastahack-python](https://github.com/brentp/fastahack-python): cython wrapper to fastahack
Fermi package, https://github.com/lh3/fermi
* [Filtlong](https://github.com/rrwick/Filtlong): quality filtering tool for long reads
* [flair](https://github.com/BrooksLabUCSC/flair): Full-Length Alternative Isoform analysis of RNA
* [flair](https://github.com/BrooksLabUCSC/flair): Full-Length Alternative Isoform analysis of RNA
* [flair](https://github.com/zalandoresearch/flair): A very simple framework for state-of-the-art Natural Language Processing (NLP)


* [FSAmisc](https://github.com/droglenc/FSAmisc): In progress or miscellaneous functions eventually destined for the FSA package
* [FuSeq](https://github.com/nghiavtr/FuSeq): A fast detection of fusion genes from paired-end RNA-seq data
* [fusioncatcher](https://github.com/ndaniel/fusioncatcher): Finder of Somatic Fusion Genes in RNA-seq data
GapCloser, http://soap.genomics.org.cn/about.html
* [gatk](https://github.com/broadinstitute/gatk): Official code repository for GATK versions 4 and up 
* [GEMINI document](http://gemini.readthedocs.io/en/latest/)
* [GEMINI](https://github.com/arq5x/gemini): integrative exploration of genetic variation and genome annotations
* [GeneFuse](https://github.com/OpenGene/GeneFuse): Gene fusion detection and visualization
* general websites
* [genomescope](https://github.com/schatzlab/genomescope): https://github.com/schatzlab/genomescope
* [GenomicConsensus](https://github.com/PacificBiosciences/GenomicConsensus): PacBio® variant and consensus caller

* [gffread](https://github.com/gpertea/gffread): GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more


* [giggle](https://github.com/ryanlayer/giggle): Interval data structure
GiniClust: https://github.com/lanjiangboston/GiniClust
* [git-history](https://github.com/pomber/git-history)
* [Gmove](https://github.com/institut-de-genomique/gmove): a gene prediction tool 
* [goleft](https://github.com/brentp/goleft): goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
* [gqt](https://github.com/ryanlayer/gqt): A genotype query interface.
* [grabix](https://github.com/arq5x/grabix): a wee tool for random access into BGZF files.
* [gui_poretools](https://github.com/andrewwhwang/gui_poretools)
* [HaMMLET](https://github.com/wiedenhoeft/HaMMLET): Fast Bayesian Hidden Markov Model with Wavelet Compression


* [hic_breakfinder](https://github.com/dixonlab/hic_breakfinder)
* [higlass](https://github.com/hms-dbmi/higlass): Fast contact matrix visualization for the web
* [HipSTR](https://github.com/tfwillems/HipSTR): Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
* [hmftools](https://github.com/hartwigmedical/hmftools): arious utility tools for working with genomics data
* [hmftools](https://github.com/hartwigmedical/hmftools): Various utility tools for working with genomics data



* [htslib](https://github.com/samtools/htslib): C library for high-throughput sequencing data formats
* [hts-python](https://github.com/quinlan-lab/hts-python): pythonic wrapper for htslib
* [humann2](https://bitbucket.org/biobakery/humann2/wiki/Home)

* [importGDC](https://github.com/ding-lab/importGDC): Command line client for Genomic Data Commons data downloads

InterProScan, http://www.ebi.ac.uk/interpro/download.html
* [Ira Hall lab](https://github.com/hall-lab)
-i reads \
IRGSP build 4, http://rapdb.dna.affrc.go.jp/download/build4.html
* [JAFFA](https://github.com/Oshlack/JAFFA)

* [javascript-algorithms](https://github.com/trekhleb/javascript-algorithms): Algorithms and data structures implemented in JavaScript with explanations and links to further readings


* [Jvarkit](https://lindenb.github.io/jvarkit/): Java utilities for Bioinformatics

* [lihang-code](https://github.com/fengdu78/lihang-code): 《统计学习方法》的代码实现

* [lordfast](https://github.com/vpc-ccg/lordfast): Sensitive and Fast Alignment Search Tool for Long Read sequencing Data

* [maf2synteny](https://github.com/fenderglass/maf2synteny): A tool for recovering synteny blocks from multiple alignment
* [maftools](https://github.com/PoisonAlien/maftools): Summarize, Analyze and Visualize MAF files from TCGA or in house studies
* [manta](https://github.com/Illumina/manta)


* [md2googleslides](https://github.com/gsuitedevs/md2googleslides): Generate Google Slides from markdown
MEGA5, http://www.megasoftware.net/index.php



* [MET-breast-landscapes](https://github.com/cclab-brca/MET-breast-landscapes)

* MiniAsm and MiniMap (https://github.com/lh3/miniasm,https://github.com/lh3/minimap/)
* [minion_qc](https://github.com/roblanf/minion_qc): Quality control for MinION sequencing data
* [MiOncoCirc](https://mioncocirc.github.io): A compendium of circular RNAs compiled from cancer clinical samples at The University of Michigan
* [monocle2-rge-paper](https://github.com/cole-trapnell-lab/monocle2-rge-paper): Scripts needed to generate the figures for the Monocle 2 paper
* [Monocle](https://cole-trapnell-lab.github.io/monocle-release/docs/)
* [mosdepth](https://github.com/arq5x/mosdepth): fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing.
mpath: https://github.com/JinmiaoChenLab/Mpath
* [MultiQC](https://github.com/ewels/MultiQC): Aggregate results from bioinformatics analyses across many samples into a single report
MUMmer, http://mummer.sourceforge.net/; ClustalW, http://www.clustal.org/
* [MuSiC2](https://github.com/ding-lab/MuSiC2): identifying mutational significance in cancer genomes
* [MuSiC2](https://github.com/ding-lab/MuSiC2): identifying mutational significance in cancer genomes





* [ncbitax2lin](https://github.com/zyxue/ncbitax2lin): Convert NCBI taxonomy dump into lineages
* [NGmerge](https://github.com/jsh58/NGmerge): Merging paired-end reads and removing adapters



* [NGTAS_pipeline](https://github.com/cclab-brca/NGTAS_pipeline): Computational pipeline to analyse Next Generation Targeted Amplicon Sequence data
* [npAnalysis](https://github.com/mdcao/npAnalysis): Realtime identification of bacterial sample



* npScarf(https://github.com/mdcao/npScarf).

* Other projects based on Japsa


* [pathogen-informatics-training](https://github.com/sanger-pathogens/pathogen-informatics-training)
* [pbalign](https://github.com/PacificBiosciences/pbalign): pbalign maps PacBio reads to reference sequences and saves alignments to a BAM file

* [PBJelly2利用Pacbio数据进行scaffolding](http://www.chenlianfu.com/?p=2270)
* [PBJelly](https://github.com/alvaralmstedt/Tutorials/wiki/Gap-closing-with-PBJelly): Gap-closing-with-PBJelly
* [pbmm2](https://github.com/PacificBiosciences/pbmm2): A minimap2 frontend for PacBio native data formats 

* pcaReduce: https://github.com/JustinaZ/pcaReduce
* [pgap](https://github.com/ncbi/pgap): NCBI Prokaryotic Genome Annotation Pipeline
* [PhageXpress](https://github.com/mdcao/phagexpress)
* PhenoGraph: https://github.com/jacoblevine/PhenoGraph
* PHYLIP, http://evolution.genetics.washington.edu/phylip.html



* [Pipeliner](https://github.com/CCBR/Pipeliner)
* [Pisces](https://github.com/Illumina/Pisces): Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows






* [professional-programming](https://github.com/charlax/professional-programming): A collection of full-stack resources for programmers
* [pyfasta](https://github.com/brentp/pyfasta)



RaceID2: https://github.com/dgrun/StemID
RaceID3: https://github.com/dgrun/RaceID3_StemID2
RaceID: https://github.com/dgrun/RaceID
* Racon (https://github.com/isovic/racon)
RAP-DB on IRGSP-1.0, http://rapdb.dna.affrc.go.jp/download/irgsp1.html
RAP-DB on IRGSP4, http://rapdb.dna.affrc.go.jp/download/build4.html
* [raxml-ng](https://github.com/amkozlov/raxml-ng): RAxML Next Generation: faster, easier-to-use and more flexible
--recursive \

RepeatMasker, http://www.repeatmasker.org/
REPLACE, ftp://ftp.sanger.ac.uk/pub/users/zn1/merge/replace/
* [restez](https://github.com/ropensci/restez): Create and Query a Local Copy of GenBank in R
RGAP 7, http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Pro
* [rkmh](https://github.com/edawson/rkmh): Classify sequencing reads using MinHash.
* [Roary](https://github.com/sanger-pathogens/Roary): Rapid large-scale prokaryote pan genome analysis 
* [RTutor](https://github.com/skranz/RTutor): Creating interactive R Problem Sets. Automatic hints and solution checks. (Shiny or RStudio)

* [samblaster](https://github.com/GregoryFaust/samblaster): a tool to mark duplicates and extract discordant and split reads from sam files

SAMtools, http://samtools.sourceforge.net/
* samtools (https://github.com/samtools/samtools)
* [sanger-pathogens](https://github.com/sanger-pathogens/sanger-pathogens.github.io)
* [SARTools](https://github.com/PF2-pasteur-fr/SARTools): Statistical Analysis of RNA-Seq Tools

SC3: http://bioconductor.org/packages/release/bioc/html/SC3.html

scanpy: https://github.com/theislab/scanpy


* [Science For Life Laboratory](https://github.com/SciLifeLab)

* [scMerge](https://github.com/SydneyBioX/scMerge):Statistical technique for removing unwanted variation from multiple scRNA-seq datasets

* [scRNA-seq-workshop-Fall-2018](https://github.com/harvardinformatics/scRNA-seq-workshop-Fall-2018)


* [seqan](https://github.com/seqan/seqan)
* [SeqArray](https://github.com/zhengxwen/SeqArray): Big Data Management of Whole-Genome Sequence Variant Calls
* [SeqArray](https://github.com/zhengxwen/SeqArray): Big Data Management of Whole-Genome Sequence Variant Calls (Development Version)
* [SeqLib](https://github.com/walaj/SeqLib): C++ htslib/bwa-mem/fermi interface for interrogating sequence data

Seurat (latest): https://satijalab.org/seurat/

SIMLR: https://bioconductor.org/packages/release/bioc/html/SIMLR.html
SINCERA: https://github.com/xu-lab/SINCERA



SMALT, http://www.sanger.ac.uk/science/tools/smalt-0


* [smithwaterman](https://github.com/ekg/smithwaterman): smith-waterman-gotoh alignment algorithm
* [Snakemake-Workflows](https://github.com/snakemake-workflows)



SNN-Cliq: http://bioinfo.uncc.edu/SNNCliq/

* [SoupX](https://github.com/constantAmateur/SoupX): R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
-s output \
* SPAdes (http://bioinf.spbau.ru/spades)
* [sparsepp](https://github.com/greg7mdp/sparsepp): A fast, memory efficient hash map for C++
* [SpeedSeq](https://github.com/hall-lab/speedseq): A flexible framework for rapid genome analysis and interpretation
* [spVCF](https://github.com/mlin/spVCF): Sparse Project VCF: evolution of VCF to encode population genotype matrices efficiently
* [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion): STAR-Fusion codebase
* [STAR-Fusion-Tutorial](https://github.com/STAR-Fusion/STAR-Fusion-Tutorial): Tutorial for STAR-Fusion, FusionInspector, and de novo reconstruction of fusion transcripts using Trinity



# Structural variants
##[superFreq](https://github.com/ChristofferFlensburg/superFreq): Analysis pipeline for cancer exomes










* [Swift-T-Variant-Calling](https://github.com/ncsa/Swift-T-Variant-Calling): use in the analysis of Whole Genome and Whole Exome Sequencing studies
* [swne](https://github.com/yanwu2014/swne): Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
* [TADbit](https://github.com/3DGenomes/TADbit)
* [tcR](https://github.com/cran/tcR): Advanced Data Analysis of Immune Receptor Repertoires
* [TE database](https://www.genome.arizona.edu/cgi-bin/rite/index.cgi)
* [TensorFlow-Course](https://github.com/open-source-for-science/TensorFlow-Course)
# tenX
* [TEPID](https://github.com/ListerLab/TEPID): Transposable element polymorphism identification
* [tetoolkit](https://github.com/mhammell-laboratory/tetoolkit): A package for including transposable elements in differential enrichment analysis of sequencing datasets.
* [The Bioinformatics Repository](https://github.com/bioinform)
-t $(nproc) \

* [Trim Galore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/): A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
TSCAN: https://bioconductor.org/packages/release/bioc/html/TSCAN.html
* [umis](https://github.com/vals/umis): Tools for processing UMI RNA-tag data
#!/usr/bin/env python
* [VarDict](https://github.com/AstraZeneca-NGS/VarDict)
* [VariantBam](https://github.com/walaj/VariantBam): Filtering and profiling of next-generational sequencing data using region-specific rules
* [vcf2phylip](https://github.com/edgardomortiz/vcf2phylip): Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
* [vcflib](https://github.com/vcflib/vcflib): a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
vera/albacore \
* [vg](https://github.com/vgteam/vg#vg): tools for working with genome variation graphs

* [viralzone](https://viralzone.expasy.org)


# websites
* [Week2 单细胞入门-听一篇Cell报告](https://vip.biotrainee.com/d/339-week2-cell)



* [xCell](https://github.com/dviraran/xCell): Cell types enrichment analysis
##* [XMas](https://github.com/mdcao/XMas): Phylogenetic distance method using information theory
* [xvfbwrapper](https://github.com/cgoldberg/xvfbwrapper): Manage headless displays with Xvfb (X virtual framebuffer)
* [单细胞转录组3大R包之monocle2](https://cloud.tencent.com/developer/article/1055888)


 
* [100,000 Genomes Project](http://www.genomicsengland.co.uk/the-100000-genomes-project/)
* [1000 Genomes Project](http://www.1000genomes.org/)
* [10x Genomics](https://github.com/10XGenomics)
* [aCNViewer](https://github.com/FJD-CEPH/aCNViewer): Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
* [Alfred](https://tobiasrausch.com/alfred/): BAM alignment statistics, feature counting and feature annotation

* [Australian Schizophrenia Research Bank: A Database of Comprehensive Clinical, Endophenotypic and Genetic Data for Aetiological Studies of Schizophrenia](https://journals.sagepub.com/doi/abs/10.3109/00048674.2010.501758?journalCode=anpa)
* [Awesome 10x Genomics](https://github.com/johandahlberg/awesome-10x-genomics)
* [Basic Local Alignment Search Tool (BLAST)](https://blast.ncbi.nlm.nih.gov/Blast.cgi)
* [bcalm](https://github.com/GATB/bcalm): de Bruijn graph compaction in low memory
* [Beagle](http://faculty.washington.edu/browning/beagle/beagle.html)
* [bs3](https://github.com/khuang28jhu/bs3): BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads
* [Cancer Cell Line Encyclopedia](https://portals.broadinstitute.org/ccle)
* [cDNA_Cupcake](https://github.com/magdoll/cdna_cupcake): Miscellaneous collection of Python and R scripts for processing Iso-Seq data


* [colocalization tests pipeline](https://bitbucket.org/mgloud/production_coloc_pipeline/) 
* [Compatible Software](https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software)

* [Data for coronary artery smooth muscle cells](https://stanford.app.box.com/s/e6e8hyft5u7wix1nzg5mjfqa084c4tin)
* [Data for retinal pigment epithelium cells](https://stanford.box.com/s/asrxy0o66xxe1j7mfj56p3z3d405gijj)
* [DataVisualization](https://gist.github.com/KestindotC/7f8caa8be6b33cbe06dbdc5b98d10d6a): Data Visualization in Bioinformatics
* [dbvar by study](https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/)
* [dbvar download](https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_assembly/GRCh38/vcf/)
* [dbvar](https://www.ncbi.nlm.nih.gov/dbvar/content/human_hub/): Human Structural Variant Data Hub
* [DECIPHER](https://decipher.sanger.ac.uk/)
* [DECIPHER](https://decipher.sanger.ac.uk)
* [DECIPHER Syndrome Overview](https://decipher.sanger.ac.uk/disorders#syndromes/overview)
* [denovo-db](http://denovo-db.gs.washington.edu/)
* [denovodb v.1.5 documentation](http://denovo-db.gs.washington.edu/denovo-db.v.1.5.pdf)
* [DenovolyzeR](http://denovolyzer.org)
* [Eagle](http://www.hsph.harvard.edu/alkes-price/software/)
* [ea-utils fastqMCF program](https://expressionanalysis.github.io/ea-utils/)
* [European Genome-phenome Archive](https://www.ebi.ac.uk/ega/home)
* [ExAC03](http://exac.broadinstitute.org)
* [ExpansionHunter](https://github.com/Illumina/ExpansionHunter): A tool for estimating repeat sizes
* [fast5seek](https://github.com/mbhall88/fast5seek): Subset of fast5 files contained in a fastq, BAM, or SAM file
* [Fast GWAS download script](https://github.com/mikegloudemans/gwas-download)
* [FxTools](https://github.com/BGI-shenzhen/FxTools): a comprehensive toolkit for FASTA and FASTQ file manipulation
* [GATK](https://www.broadinstitute.org/gatk/)
* [Gene2MeSH](http://ws.ncibi.org/g2m.html)
* [GeneCards](https://www.genecards.org/)
* [GenomeDK high-performance-computing cluster in Denmark](https://genome.au.dk/)
* [genome-in-a-bottle](https://github.com/genome-in-a-bottle): A public-private-academic consortium hosted by NIST to develop reference materials and standards for clinical sequencing
* [Genomic Regions Enrichment of Annotations Tool](http://great.stanford.edu/public/html/splash.php)
* [/giab/ftp/data/NA12878](https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/)
* [Github code for SV identification](https://github.com/dixonlab/hic_breakfinder)
* [GOrilla](http://cbl-gorilla.cs.technion.ac.il/)
* [gramtools](https://github.com/iqbal-lab-org/gramtools): Genome inference from a population reference graph
* [Graphtyper](https://github.com/DecodeGenetics/graphtyper)
* [GTEx eQTL data](https://gtexportal.org/home/datasets)
* [GTEx portal](https://gtexportal.org/home/)
* [H3ABioNet](https://github.com/h3abionet)
* [h3agwas](https://github.com/h3abionet/h3agwas): GWAS Pipeline for H3Africa
* [hapfuse](http://bitbucket.org/wkretzsch/hapfuse/src)
* [HAPI-UR](http://code.google.com/p/hapi-ur/)


* [HipSTR](https://github.com/tfwillems/HipSTR): Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
* [hmftools](https://github.com/hartwigmedical/hmftools): Various utility tools for working with genomics data

* [ID Gene Database Project](http://gfuncpathdb.ucdenver.edu/iddrc/iddrc/home.php)
* [IGSR: The International Genome Sample Resource](http://www.internationalgenome.org/data#download)
* [International Paediatric and Congenital Cardiac Codes](http://www.ipccc.net/)
* [InterVar](https://github.com/WGLab/InterVar): A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
* [IPD-IMGT/HLA](http://www.ebi.ac.uk/ipd/imgt/hla/): https://github.com/ANHIG/IMGTHLA
* [iPSYCH download site](http://ipsych.au.dk/downloads/)
* [iPSYCH project](http://ipsych.au.dk/)




* [LISA cluster at SURFsara](https://userinfo.surfsara.nl/systems/lisa/)
* [Lisa Genetic Cluster Computer](http://geneticcluster.org/)
* [LocusCompare](http://locuscompare.com): https://github.com/boxiangliu/locuscompare.
* [LocusCompareR](https://github.com/boxiangliu/locuscomparer)
* [LRRC14B](https://www.genecards.org/cgi-bin/carddisp.pl?gene=LRRC14B)
* [maf2sam](https://github.com/peterjc/maf2sam): Convert MIRA Assembly Format (MAF) to Sequence Alignment/Map (SAM) format

* [MetaSVM/ANNOVAR](http://annovar.openbioinformatics.org)

* [Michigan Imputation Server](http://imputationserver.sph.umich.edu/)
* [mrsFAST-ultra](https://sfu-compbio.github.io/mrsfast/): map short reads to reference genome assemblies in a fast and memory-efficient manner
* [Multiple geom_rect over a time series](https://stackoverflow.com/questions/32021398/multiple-geom-rect-over-a-time-series)
* [NCBI-Hackathons](https://github.com/NCBI-Hackathons)

* [NHLBI ESP](http://evs.gs.washington.edu/EVS/)
* [NIMH Repository](https://www.nimhgenetics.org/available_data/autism/)
* [Nonredundant_Structural_Variants](https://github.com/ncbi/dbvar/tree/master/Structural_Variant_Sets/Nonredundant_Structural_Variants)
* [Online Mendelian Inheritance in Man (OMIM)](https://www.omim.org)
* [Pacific Biosciences](https://github.com/PacificBiosciences)
* [PGC download site](https://www.med.unc.edu/pgc/results-and-downloads/)
* [PhylDiag](https://github.com/DyogenIBENS/PhylDiag): From the comparison of two extant genomes and corresponding gene families, PhylDiag detects conserved segments, i.e. segments of chromosomes unbroken during evolution
* [plink 1.9](http://www.cog-genomics.org/plink/1.9/)
* [PLINK2]h(ttp://www.cog-genomics.org/plink2)



* [pufferfish](https://github.com/COMBINE-lab/pufferfish)
* [repbase](https://www.girinst.org/downloads/)
* [Replication Domain](https://www2.replicationdomain.com/index.php)
* [R package ‘propagate’]( https://CRAN.R-project.org/package=propagate)
* [rtg-tools](https://github.com/RealTimeGenomics/rtg-tools): Utilities for accurate VCF comparison and manipulation

* [samblaster](https://github.com/GregoryFaust/samblaster):  a tool to mark duplicates and extract discordant and split reads from sam files
* [Sanger Imputation Service](http://imputation.sanger.ac.uk/)
* [SFARI Gene](https://gene.sfari.org/)

* [SNPweights](http://www.hsph.harvard.edu/alkes-price/software/)
* [SpeedSeq framework](https://github.com/hall-lab/speedseq)
* [St.Jude Cloud](https://pecan.stjude.cloud/#/home)


* [szdb](http://www.szdb.org/): a database for schizophrenia genetic research
* [SZGR](https://bioinfo.uth.edu/SZGR/)

* [The phase 3 structural variant dataset download](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/)
* [The phase 3 structural variant dataset source ](http://www.internationalgenome.org/phase-3-structural-variant-dataset/)
* [TitanCNA](https://github.com/gavinha/TitanCNA): Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
* [trio binning](https://obj.umiacs.umd.edu/marbl_publications/triobinning/index.html)
* [TrioDeNovo](http://genome.sph.umich.edu/wiki/Triodenovo)
* [UK10K project](http://www.uk10k.org/)
* [UK Biobank genotyping and quality control documentation](http://www.ukbiobank.ac.uk/wp-content/uploads/2014/04/UKBiobank_genotyping_QC_documentation-web.pdf)
* [UK Biobank](http://www.ukbiobank.ac.uk/)

* [Variant Normalization](https://genome.sph.umich.edu/wiki/Variant_Normalization)
* [VEP: Variant Effect Predictor](https://asia.ensembl.org/info/docs/tools/vep/index.html)
* [vg](https://github.com/vgteam/vg)
* [virus pathogen resource](https://www.viprbrc.org/brc/home.spg?decorator=vipr)