生信分析常用軟體記錄

20190727，在學習二代分析的過程中，只是根據別人已經建好的輪子照抄照搬，並不能真正理解每一步為什麼要用這個軟體，以及軟體之間的區別。因此今天記錄一些生信分析過程（主要是二代測序）中常用的軟體，若有時間去檢視一下每個軟體的功能、官方介紹和演算法等。

不按順序的雜亂記錄

sd linux安裝軟體

r, tanperl5lib, augustus-3.3.2, bamtools-2.4.2, bedops_linux_x86_64-v2.4.36, bismark_v0.22.1,

boost_1_69_0, bowtie-1.2.2-linux-x86_64, braker-2.1.2, circos-tutorials-0.67, clineff-notinstalled,

cmake-3.13.4-linux-x86_64, cufflinks-2.2.1.linux_x86_64, gapcloser-v1.12-r6, geneid-1.4.5,

genemark-et-4.38, gff3toolkit-1.4.4, gfftools-6bde56e, glimmerhmm-3.0.4, lastz-1.04.00,

mauve_snapshot_2015-02-13, mummer3.23, mummer-4.0.0beta2, ngsqctoolkit_v2.3.3,

ngs-tools-master, novocraft-3.09.02, orthomclsoftware-v2.0.9, picard-tools-1.124, quake,

repeatmasker-4.0.8, rmblastn-2.2.28, snpeff_latest_core, snpeff-4.2, snpeff-4.3t, soapdenovo2-src-r240,

sratoolkit.2.9.2-centos_linux64, star-2.7.0e, stringtie-1.3.5.linux_x86_64, tophat-2.1.1.linux_x86_64,

trimmomatic-0.39, trnascan-se-2.0, vgsc2

lh linux安裝軟體

bcftools, bowtie, bwa, circo, gatk, mummer, picard, samtools-1.2, snpeff-4.0, tophat_cufflinks

hsx linux安裝軟體

123sv-0.9, armatus-2.2, armatus-master, augustus-3.0, bcftools-1.3.1, biopython-1.63,

bioscripts-master, boost_1_58_0, boost_1_70_0, brat_bw-2.0.1, brat_nova, breakdancer-1.1.2, bwa-0.7.7,

chrom3d-master, class-std-0.013, clever-toolkit-v2.0rc3, cmake-3.2.3, config-std-0.901, deepvariant-r0.7,

dwac-seq0.7, enter, gen_scan, genomeanalysistk, google-cloud-sdk, htslib-1.3.1, htslib-develop,

i**_2.3.31, interproscan-5.2-45.0, interval-1.0.0, ipython-1.1.0, jinja2-master, nose-1.3.0, numpy-1.7.2,

picard-tools-1.108, popbam, primer3-2.3.7, primer3-py-0.3.0, primer3-py-0.5.1, pygments-1.6, pyqt-gpl-5.2

python-2.7.12, pyzmq-14.0.1, pyzmq-master, qt-everywhere-opensource-src-5.2.0, r-3.0.1,

repeatmasker, sip-4.15.4, tanghaibao-mcscan-4cfe0f5