usually bioinformatics tools

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

This directory contains applications for stand-alone use, built specifically for a Linux 64-bit machine. For help on the bigBed and bigWig applications see: http://genome.ucsc.edu/goldenPath/help/bigBed.html http://genome.ucsc.edu/goldenPath/help/bigWig.html View the file ‘FOOTER’ to see the usage statement for each of the applications. Name Last modified Size Description Parent Directory – FOOTER 12-Jun-2012 18:01 65K bedClip 12-Jun-2012 18:01 […]

June 14th, 2012 | Tags: , | Category: 二代测序, 生物信息 | Leave a comment

ubuntu 9.10 下安装glimmer3失败及其解决办法

(1)安装前，先修改src/Common下第26行#include <string> 为 #include <cstring>；再make，可是仍然会产生以下错误 * Make Target is all ##### Making Directory /usr/local/glimmer3.02/src/Common all ##### make[1]: 正在进入目录 `/usr/local/glimmer3.02/src/Common’ @@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@ @@@@@@@@@@@@@@@@@@@ fasta.cc @@@@@@@@@@@@@@@@@@@@@ @@@@@@@@@@@@@@@@@@@ gene.cc @@@@@@@@@@@@@@@@@@@@@ gene.cc: In member function ‘void PWM_t::Print(FILE*)’: gene.cc:263: warning: deprecated conversion from string constant to ‘char*’ gene.cc: In function ‘int Char_Sub(char)’: gene.cc:448: error: invalid conversion from ‘const char*’ […]

June 12th, 2012 | Tags: , | Category: 服务器管理, 生物信息 | Leave a comment

Bpipe A tool for running and managing bioinformatics pipelines

Starting from a Shell Script

In this tutorial we will develop a Bpipe pipeline script for a realistic (but simplified) analysis pipeline used for variant calling on NGS data. In this pipeline the following stages are executed:

sequence alignment using bwa sorting and indexing output files using samtools PCR duplicate removal using Picard calling variants […]

May 17th, 2012 | Tags: , | Category: 生物信息 | Leave a comment