生信分析常用软件记录

20190727，在学习二代分析的过程中，只是根据别人已经建好的轮子照抄照搬，并不能真正理解每一步为什么要用这个软件，以及软件之间的区别。因此今天记录一些生信分析过程（主要是二代测序）中常用的软件，若有时间去查看一下每个软件的功能、官方介绍和算法等。

不按顺序的杂乱记录

sd linux安装软件

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安装软件

bcftools, bowtie, bwa, circo, GATK, MUMmer, picard, samtools-1.2, snpEff-4.0, tophat_cufflinks

hsx linux安装软件

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,

IGV_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