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  1. Speed up sequence alignments using your video card!
  2. Bioinformatics
  3. Software packages for next gen sequence analysis
  4. SOAP: short oligonucleotide alignment program.
  5. Sample short read data set?
  6. Bioconductor for next-gen sequencing anlaysis?
  7. Preliminary benchmark of different alignment programs
  8. solexa small rna questions
  9. Who is Geospiza?
  10. New version of Solexa GA pipeline tool
  11. FindPeaks 3.1.3 (alpha) - ChIP-Seq and UCSC-compatible short-read wig track creator
  12. pooling genes in a solexa lane
  13. ISMB 2008 SIG on Algorithms for Next Gen Sequencing
  14. Quality score threshold?
  15. Converting FASTQ to RMAP prb files
  16. SoftGenetics NextGENe
  17. CLC Genomics Workbench
  18. short reads missed by aligners
  19. Solexa data to fasta
  20. eland realign file
  21. Illumina's PRB file to FastQ
  22. indels using single end short reads!
  23. where can I download eland program?
  24. Fasta to Ace conversion
  25. Using pbShort
  26. Maq and export format
  27. SeqMan NGen
  28. New Short Read Aligner
  29. Desktop computer specs for routine analyses? Post your rig
  30. Questions about solexa quality score
  31. Questions about solexa quality score！
  32. compare solexa and 454
  33. Plug for new ChIP-Seq Package and the Integrated Genome Browser
  34. Heavy read stacking on the solexa platform
  35. question about ssaha
  36. Paired-end Illumina data
  37. FindPeaks (ChIP-Seq) update
  38. Convert euler-sr output to amos-bank
  39. population genetics parameter estimation of solexa population sequencing
  40. Human reference sequence and tools like MAQ
  41. Interpretation of Euler-SR assembly (454 transcriptome)
  42. SNP Allele-Frequency Determination in Pooled DNA Samples using solexa
  43. de novo assembly of transcriptomes
  44. Any programme can estimate SNP frequency ?
  45. What does Illumina raw data look like?
  46. Allpaths installation and usage
  47. Bioinformatics at COMSATS IIT
  48. Reference Genome
  49. spike-in data set
  50. Genomatix offerings
  51. reference set for analyzing illumina DpnII tags?
  52. How to detect real deletion or gaps in sequencing projects
  53. retrieve gene name
  54. de novo hybrid assembly
  55. An HMM approach to genome-wide identification of differential histone modification si
  56. different Illumina convention in fastq files?
  57. Mapping benchmarks of the GMS
  58. maq on a mac
  59. how to use soap?
  60. Public Helicos Data
  61. SOAP on Mac Pro
  62. Gene Expression Tag Table Software Now Available
  63. Running MAQ SNP/Indel detection/Assembly Tools on short aligners
  64. what is a paired-end read?
  65. Velvet de novo assembly to amosvalidate
  66. ZOOM released (supporting both Illumina data and ABI SOLiD data)
  67. Alta-Cyclic
  68. what is wrong with my MAQ?
  69. ShortRead package
  70. ChIP-Seq reads correlated/distance to with TSS/promoter etc.
  71. Methods for comparing RNA sequencing libraries?
  72. MAQ and indel detection
  73. Transcriptom assembly
  74. MAQ SNP calling
  75. MAQ mapping quality scores
  76. FindPeaks is now OpenSource!
  77. installation can't find TRF programme
  78. export from MAQ to EagleViewer
  79. finding polymorphisms by large sequence alignments
  80. LastGen Assembly
  81. Data retention
  82. Swift: Open source primary data analysis for Next-gen sequencers
  83. new basecallers since Bustard
  84. RNA-seq and normalization numbers
  85. from CGH arrays to genome map
  86. Analysis of Solexa multiplexed data
  87. SNP/Mutation Detection Using Illumina Paired-end Data
  88. why reads piled up at repeat region?
  89. eland_tag - 3' tag analysis
  90. Maq SNP filtering script bug?
  91. Eland-to-Bed algorithm
  92. Hybrid sequencing assembly visualization
  93. eland2maq
  94. alignment reference
  95. SNP calling on 454 data
  96. ChipSEQ on Solexa (low % align, unusable reads)
  97. Quality score graph
  98. Bowtie, an ultrafast, memory-efficient, open source short read aligner
  99. SOLiD alignment browser
  100. Maq problems getting started
  101. MAQ .map alignment format converter
  102. How to use MAQVIEW?
  103. How to make great wiggle plots and Seq figures
  104. Structural Variations
  105. Maq SNP calls from a large pool
  106. Slider - Maximum use of probability information for alignment of short sequence reads
  107. paired-end reads and shotgun
  108. Inversions
  109. BFAST: Blat-like Fast Accurate Search Tool for Large-Scale Genome Resequencing
  110. ABI Color Space to Bases
  111. CisGenome -- an integrated tool for ChIP-seq data analysis
  112. eagleview discrepancy search
  113. Analysis for Paired end reads
  114. SNP Frequency
  115. start position of reads and its distribution
  116. Pipeline Illumina question
  117. Segmentation Fault from Maq's .map files
  118. maq map - Assertion 'matches' failed
  119. 1000 genomes fastq format
  120. ChIP seq
  121. Need comment on CLCbio software
  122. LIMS Systems
  123. Paired end solexa (goat/gerald) pipeline
  124. Reference seq. on MAQviewer
  125. Help installing Illumina pipeline 1.0
  126. Input files for the Celera Assembler?
  127. indelpe from MAQ
  128. How to estimate the transcription level?
  129. still got Maq problems
  130. Celera Assembler (WGS) - splice site file?
  131. de novo 454 assembly
  132. Assess the quality of solexa reads
  133. new EULER-SR
  134. Maq output: assemble.log file contains what?
  135. MAQ Scores & Quantify maq alignments?
  136. Solid VS Solexa
  137. a question about fasta quality.
  138. GapPipeline v1.0 on Mac OS X 10.5.5
  139. SAM: a generic alignment format
  140. Raw solexa data processing
  141. Convert MAQ or Bowtie output to Vmatch
  142. MAQ: finding the stop position of an alignment
  143. Solexa anomaly.txt for structual variants
  144. ALLPATHS compiling issues
  145. Novoalign V2.0 Released
  146. how to view a 600MB wig file
  147. Gene Calling
  148. Illumina de novo assembly with quality values
  149. MAQ Alignment Depth
  150. New software: G-Morse : Annotating genomes with massive-scale RNA-sequencing
  151. Assembling .sff files from 454 and finishing
  152. Eland to ACE
  153. Tag (string) Compression Techniques
  154. Alignment Questions
  155. MapView: a viewer for short reads alignment
  156. Cisgenome
  157. Help - MAQ getting started
  158. ChIP-Seq Challenge
  159. A question about alignment depth
  160. Alignment of Long SAGE tags
  161. miRNA aligning/counting
  162. Bowtie print read length
  163. Fraction of reads incorporated in Velvet assemblies
  164. BS-Seq Public /Sharing Data
  165. Shore
  166. CAP3 output *.ace in EagleView?
  167. Assembling pooled BACs from 454 data
  168. About Data Format and Eland Input
  169. Amplification region in genome
  170. Solexa pipeline
  171. How to convert .txt file to .bed or .gff, How can we use chip seq data in R software
  172. Tool for Sorting PRB file
  173. Updated How to convert .txt file to .bed .GFF or .BAR file format,
  174. problems concerning seq.txt and prb.txt
  175. Vaal
  176. User friendly ChIP-Seq software
  177. Reference genome for MAQ - split reference genome by chromosome or not?
  178. bowtie - windows instalation
  179. Maqview Reference Sequence
  180. What is the difference between sol2std and sol2sanger
  181. illumina GA2, 75bp paired-end data
  182. MAQ - segmentation error
  183. help - buffer overflow problem of Maq in Ubuntu 8.10
  184. What NextGen LIMS do you use?
  185. Parallel Processing for Sequence Analysis
  186. SOAP output format - description?
  187. Question about pthred quality
  188. CpG Islands Vs CHIP-Seq data
  189. SOAP vs Bowtie output
  190. MAQ mapstat error rate
  191. How to using euler-sr to assebling 454 seq?
  192. maq with no mismatches
  193. Eland for Tag Greater than 32 basepair
  194. How to trim the adaptor sequence from the solexa small RNA sequencing data?
  195. Data Format Question
  196. .bam alignment format from 1000 Genomes Project
  197. Viewing paired-end inconsistencies in 454 scaffolds
  198. Strange maq 7.1 problem
  199. Eland output from SeqMap
  200. chord->getLength Newbler error
  201. All chromosomes and maq
  202. Eland for different sizes
  203. view .wig files
  204. MAQ error
  205. Maq problem: 0 raw reads mapped
  206. PubMed: PASS: a Program to Align Short Sequences.
  207. Setting up a 454 Bioinformatics center
  208. maq compile error on Ubuntu
  209. Fastq quliaty score and MAQ output quality score
  210. mapping 454 reads to a reference genome
  211. Solexa.abi and 454 seq data.
  212. long repeated elements in a bacterial genome
  213. Maq Alignment Coordinates
  214. de novo assembly on 3.5Gbp data -- computational speed!!??
  215. comparing results from two different reference genomes
  216. Alignment of ABI solid reads and 454 reads
  217. BOWTIE output problems
  218. Two Version of Solexa Quality Score Formula
  219. maq pair end alignment error
  220. sff_extract paired end extraction error
  221. MAQ and small RNAs
  222. Burrows-Wheeler Aligners for Colorspace?
  223. INDEL searches!
  224. Uniquely mapped short reads (MAQ)
  225. Transcriptome assembly using solexa reads
  226. Manually correct heterozygous indels
  227. So many software for alignment!!!
  228. Euler SR
  229. Pseudocode for Generating Synthetic Tags with Error Rate
  230. Convert MAQ,SOAP alignment result to ACE format
  231. why is paired-end alignment support so important
  232. maq mapcheck
  233. A list of available sequence annotation tools?
  234. Binning of aligned mRNA-reads into gene models
  235. WIG files
  236. (a) Background Read Distribution (b) Spike-ins
  237. ISAS Alignment Software
  238. Maq multiple map output (-H)
  239. Adequate coverage for genome wide pair end sequencing
  240. Which quality score?
  241. velvet
  242. Perfect match disagreement between bowtie and BLAT on human genome
  243. BFAST - Alignment for ABI or Illumina sequencing - with qualities
  244. GBrowse and Chip-seq Peaks
  245. Software for Sorting SNPs/ InDels by Affect?
  246. FindPeaks output
  247. Segmentation fault with Mosaik
  248. Storage Gotchas
  249. Coverage display?
  250. Problem with adding 454 reads with cross_match