Preface |
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Chapter 1 Preparing Your Computing Environment |
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1 | (16) |
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1.1 Buying Your Own Computer |
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1 | (3) |
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1.2 Setting up a Computing Server |
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4 | (2) |
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1.3 Establishing a Remote Connection to a Server |
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6 | (11) |
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Chapter 2 Learning Basic Linux Commands |
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17 | (42) |
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2.1 No Need to be a Linux Guru to use Linux Effectively |
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17 | (1) |
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2.2 Folder (Directory) Operations |
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18 | (14) |
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Controlling your command prompt |
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25 | (7) |
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32 | (7) |
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2.4 Assignment of Permissions |
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39 | (8) |
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46 | (1) |
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2.5 Understanding System Status |
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47 | (7) |
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UNIX redirection and pipes |
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52 | (2) |
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2.6 Other Useful Commands |
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54 | (5) |
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Chapter 3 Checking Sequence Quality |
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59 | (22) |
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3.1 Basic High-throughput Sequencing |
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59 | (2) |
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3.2 Challenges of High Throughput Genome Sequencing |
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61 | (1) |
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3.3 Standards of Quality Score |
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62 | (3) |
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65 | (16) |
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65 | (7) |
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72 | (9) |
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Chapter 4 Sequence Alignment |
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81 | (36) |
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4.1 The Purpose of Sequence Alignment |
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81 | (2) |
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83 | (1) |
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4.2 Selection of the Sequence Alignment Tools |
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83 | (7) |
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85 | (3) |
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The BWT encoding-decoding algorithm |
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88 | (2) |
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4.3 Actual Operation of the Sequence Alignment |
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90 | (9) |
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Download and installation of Bowtie |
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90 | (6) |
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Executing sequence alignment |
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96 | (3) |
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4.4 Sequence Alignment Results File Conversion |
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99 | (9) |
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99 | (9) |
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4.5 Using the Genome Browser |
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108 | (9) |
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Chapter 5 Speeding-up with GPUs |
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117 | (30) |
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5.1 Computational Advantages of the Graphics Card |
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117 | (2) |
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5.2 Industry Standards and Usage of GPU Computing |
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119 | (19) |
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5.3 Practical CUDA Applications in Bioinformatics |
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138 | (7) |
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Preparing the reference sequence |
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140 | (3) |
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Alignment with CUSHAW2-GPU |
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143 | (2) |
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5.4 The Reason for the Limited Success of GPUs |
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145 | (2) |
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Chapter 6 Establishing a Research Workflow Pipeline |
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147 | (30) |
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6.1 Automating Your Computational Workflow |
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147 | (1) |
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148 | (9) |
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150 | (7) |
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6.3 Testing and Debugging |
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157 | (5) |
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Keeping track of the current project |
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158 | (1) |
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Complementing tests of code blocks |
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159 | (1) |
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Calculating the execution time |
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160 | (2) |
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6.4 Implementation Case Studies |
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162 | (8) |
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6.5 Case Study of Common Mistakes |
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170 | (7) |
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Mistake 1: Confusing mess of relative paths |
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170 | (2) |
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Mistake 2: Failure to change the necessary permissions |
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172 | (1) |
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Mistake 3: The disk becomes full during execution |
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172 | (2) |
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Mistake 4: Ignoring cross-platform shell portability considerations |
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174 | (3) |
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Chapter 7 Using a Bioinformatics Cloud Computing Platform |
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177 | (58) |
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7.1 Simple Introduction to the Cloud Computing Platform |
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177 | (1) |
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178 | (4) |
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7.3 Bioinformatics Cloud Computing Platforms |
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182 | (33) |
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Logging in to use Galaxy services |
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184 | (3) |
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187 | (8) |
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195 | (7) |
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Execution of sequence alignment |
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202 | (3) |
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Selecting other Galaxy servers |
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205 | (2) |
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Design and use of research workflows |
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207 | (1) |
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Establishing new research workflows |
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207 | (2) |
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Sharing and publishing process |
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209 | (3) |
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Execution of research workflows |
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212 | (1) |
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Downloading or exporting research workflows |
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212 | (2) |
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Importing research workflows |
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214 | (1) |
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7.4 Installing and Setting up your Own Galaxy Server |
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215 | (21) |
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Downloading the latest version of the Galaxy |
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216 | (1) |
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Starting your Galaxy server |
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217 | (3) |
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Allowing external execution |
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220 | (1) |
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Installation of bioinformatics tools |
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220 | (9) |
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Adding new reference sequences |
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229 | (7) |
Appendix Learning Regular Expressions through Practising Simple Data Processing |
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235 | (24) |
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236 | (1) |
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One character pattern match |
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236 | (1) |
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Numbering a file and printing line number of a hit |
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236 | (1) |
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Counting number of grepped hits |
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237 | (1) |
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UNIX redirection using pipes |
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237 | (1) |
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Grep and output several lines of context around the hit |
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237 | (1) |
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Grepping for non-matching lines |
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238 | (1) |
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Grepping for unwanted characters |
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238 | (1) |
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238 | (1) |
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Egrep or grep -E extended regular expression grep |
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239 | (1) |
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Egrep and the character class |
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239 | (1) |
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Egrep character class negation |
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240 | (1) |
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Regular expression: Beginning of line anchor ˆ |
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241 | (1) |
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Case-sensitive and case-insensitive grep |
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241 | (1) |
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Regular expression: End of line anchor |
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242 | (1) |
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More about regular expressions |
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242 | (2) |
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Even more regular expression |
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244 | (1) |
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Substitution with SED Awk and Perl |
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244 | (6) |
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Using Excel to do data processing |
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250 | (9) |
Index |
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259 | |