View Full Version : De novo discovery

Pages : [1] 2

  1. PubMed: De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using
  2. de novo 454 assembly w/ newbler ... how long?
  3. newbler assembly ... padding and SNPs
  4. De Novo plant Bac sequencing
  5. Solexa + 454 hybrid assembly
  6. De Novo Short Read Assembler?
  7. Velvet and long Illumina reads
  8. De Novo Assembly of a transcriptome
  9. a GB genome with SE PE data
  10. titanium vs standard chemistry for BAC assembly
  11. Using Velvet options and the results, examine contigs
  12. De novo short read assembly? Which assembler is the best?
  13. illumina de novo txome assm: overlapping paired ends or long inserts?
  14. Questions for Newbler users ?
  15. Newbler de novo assembly and repeats
  16. Choice of hash length k in velvet
  17. Urgent question about sequence assembly
  18. velvet and SOAPdenovo assembly
  19. Discussion about MIRA hybrid assembly of 454 reads with Illumina unpaired data
  20. Snp discovery without a reference
  21. Scaffolding output from a velvet assembly of SOLiD data
  22. de novo assembly and Illumina read length
  23. Using Vmatch to combine assemblies into a non-redundant set of contigs
  24. Velvet de novo assembly of Solid reads HOWTO
  25. Assembly of Large Genomes using Cloud Computing by Contrail
  26. Getting started with de novo genome sequencing
  27. Insert size important?
  28. newbler assembly of mated reads (FASTA format)
  29. Oases: De novo transcriptome assembly of very short reads
  30. Benchmark (or experience) between SOAPdenovo, Velvet, Abyss, and ALLPATHS2
  31. velvet denovo
  32. Velvet Parameters
  33. velvet
  34. building scaffolds using a contig and mate pair
  35. New paper: Expression profiling without reference genome / transcriptome
  36. Tag Sequence for 454 data
  37. combined assembly with Seqman Pro
  38. Scaffolding mira contigs
  39. Velvet -output format
  40. velvet N50
  41. de novo... beginner questions.
  42. gsAssembler behaving funny with PE data
  43. Need help on soap denovo
  44. mixing long and short sequences
  45. optimal k value?
  46. heterogenous data and Euler-SR
  47. Designing de-novo sequencing projects
  48. Optimal high performance computer spec for NGS data analysis
  49. How to bridge genome gaps resulting from repeats?
  50. MCF-7 Cell Line Transcript Reference Annotation Needed
  51. mira quality scores
  52. Minimus2/nucmer assembly
  53. Single End vs Paired End
  54. Chromosome assembly with next-gen data?
  55. Question on mapping reads
  56. A tad bit confused....
  57. Stats from SOAPdenovo output files
  58. Hybrid assembly w/ minimal RAM
  59. Velvet - hybrid assembly failure
  60. fast short read assembler w/ quality scores
  61. cDNA read map parameter for gsAssembler
  62. De novo assembly strategy
  63. Small RNA data analysis
  64. Velvet assembly
  65. ask for help on soap
  66. reference-free SNP discovery
  67. Optimal k-mer and N50?
  68. Gap Problems with Velvet1.0
  69. Paired-end questions
  70. how to get the genome coverage of assembly result
  71. Big Genomes and Velvet
  72. [ABySS] Odd histogram of mate-paired reads
  73. What coverage is enough??
  74. de novo assembly of polyploid genomes?
  75. Why using k-mer?
  76. Coverage required for SNP detection?
  77. bed file comparison?
  78. how to remove N (gap) in sequences?
  79. Contigs rearrangement
  80. Has anyone used the Genovo assembler?
  81. Antarctic nematode conundrum!
  82. cap3 and pcap question
  83. CisGenome for de novo motif discovery
  84. PacBio AHA hybrid assembler
  85. Velvet & paired-ends
  86. Targeted de novo assembly
  87. SNP detection (no reference) parameters
  88. Newbler de novo assembly
  89. Not getting satisfing results in SOAPde-novo
  90. Newbler Trim Status
  91. Genome size estimation
  92. rna sample
  93. short read assembly
  94. differential expression for de novo
  95. Velvet and coverage range
  96. Large K-mer Velvet
  97. transcription factor discovery on fungus
  98. Newbler2.3 & cDNA assembly
  99. Puzzling result from Illumina 150bp PE reads
  100. De Novo Assembly using Ray
  101. Euler 2.0
  102. What is the meaning of pair ends for de novo assembly?
  103. multiple k-mer & oases
  104. What approach for ~700Mb genome?
  105. looking for isoforms
  106. advice from more experienced users
  107. de novo assembly using Trinity versus Velvet-Oases
  108. how to resolve repeat areas with Velvet when doing de novo assembly
  109. Unused reads in SOAPdenovo
  110. estimate differential expression
  111. How to confirm SNPs results from a proteomics approach
  112. Trinity - de novo transcriptome assembler
  113. Coverage required for Sanger based SNP detection and Genotyping
  114. Canonical direction and assembly
  115. Velvet and reads from different generations of Illumina
  116. Alternate contig scaffoldings with ABySS
  117. used and unused reads in velvet
  118. nearly identical sequence in Celera contigs
  119. merging paired reads - any software out there?
  120. to complete or not to complete
  121. How to get assembly metrics from (AMOS) minimus and minimo assemblies?
  122. Centromeric and Telomeric Sequences
  123. The best genome de novo assembly software using hybrid data (Illumina, 454 & Sanger)?
  124. Finding of novel small RNA
  125. [Velvet,assembly] core dumped occured by runnning velvet
  126. problem with simple assembly using Velvet
  127. how complete is the draft assembly? cegma?
  128. How to Estimate the Average Coverage per RAD Locus
  129. Improvements to assembled genome
  130. K-mer abundance and mapping score
  131. the N50 is so low from soapdenovo
  132. Merging genomic Assemblies
  133. Genotyping By Sequencing (GBS) and SNP calling
  134. Problem with false SNP identification?
  135. Finding differences in gene content with Illumina SRA?
  136. Reference guided assembly
  137. De novo transcriptome quality metrics?
  138. De novo SNP calling in absence of complete reference assembly
  139. Finding *new* regions of DNA in genome assemblies
  140. parameter set of bwa-samtools for snp calling
  141. Bambus2 Input files
  142. Low coverage sequencing, which strategy?
  143. Velvet Interpretation
  144. SOAPdenovo error "cant find kmer"
  145. de novo or not de novo
  146. [help] de novo Genome Assembly : beginner
  147. Reads quality scoring system used ??
  148. Reference-guided scaffolding Bambus2
  149. NGS in population studies
  150. soapdenovo singletons??
  151. Trinity transcript naming
  152. Hybrid assembly with Illumina and SOLiD data
  153. Consensus Transcriptome
  154. A new fruitfly genome de novo sequencing
  155. trinity error
  156. velvet parameter setting
  157. Ray crash: how to debug?
  158. How to decide on a reference genome
  159. Oases Question
  160. contigs to fully assembled genome
  161. Trinity Help
  162. SOAPdenovo -reference genome
  163. using EST library as extra information
  164. From RNA-seq reads / alignments to GFF files
  165. De novo assembly from DNA sequence and RNA seq
  166. cloud computing sever for DNA sequence assembly
  167. sam created by amos bank2contig has negative start positions
  168. SOAPdenovo-Trans: Seg fault
  169. How to calculate RPKM of de novo assembled sequences
  170. DeNovo WGA sequencing of diploid Drosophila
  171. Downstream analysis for Differential Expression..
  172. ask for idea about de novo genome
  173. how to calculate the genome heterozygosity
  174. Can't get Ray working
  175. Sequencing of the Mangifera indica genome
  176. Oases Help
  177. estimate genome size through kmer analysis
  178. AllPaths-LG
  179. identifying motifs from set of up stream sequences
  180. Mapping to subsets of a transcriptome reference?
  181. SOAPdenovo Scaffolding
  182. package of phrap/phred/consed
  183. How compare together 3 partial genomes?
  184. OneMap for genetic mapping of outbred crosses - anyone?
  185. velvetg "irregular sequence" error
  186. Assembly of multiple BACs
  187. Trinity transcriptome assembly
  188. [ABySS] Problems with LSF and ABySS 1.3.4
  189. Mapping to related species
  190. Aligning genomic reads to transcriptome assembly
  191. 10 kb plasmid de novo assembly
  192. Minia: ultra-low memory contigs assembly
  193. Velvet segmentation fault
  194. ArXiv: Optimal Assembly for High Throughput Shotgun Sequencing
  195. very small N50 values from preliminary assembly of bacterial genome
  196. Velvet tests using ILM DH10B data
  197. Sequencing Degenerate Sequences
  198. MIRA Question: Improving 454 assembly with RNAseq data
  199. I will be crazy: Help about SNPs and tree!!!!
  200. New hardware for Oases: how much memory?
  201. Velveth flag question
  202. Pseudocontig and annotation transfer
  203. Soapdenovo stops at reading reads
  204. Best euthanasia method for RNA-Seq in a reptile
  205. 20kb Plasmid Assembly
  206. Gene name assignment/ Merge genome-based assembled transcripts with de novo transcrip
  207. Trinity: option to increase bowtie memory allocation
  208. biais in GC content with illumina
  209. de novo assembly with MIRA and 454 single-end reads. Too much contigs
  210. Using SOPAdenovo: no [LIB] in file
  211. Best strategy for 6 Gb de novo genome assembly?
  212. Ray : Segmentation fault (11)
  213. Ray : Segmentation fault (11)
  214. de novo assembler for se 36 bp illumina reads
  215. SOAPdenovo and FASTA files - Newbie question
  216. Unannotated sequence
  217. using data from multiple platforms/technologies
  218. what is indelFS and indelQD in the filter column of VCF file
  219. Combining two different assemblies
  220. Miseq v2 PE library length for Allpaths-LG
  221. De novo assembly
  222. One result per line for blastp?
  223. Velveth and velvetg.
  224. Denovo RNA-Seq assembly using Velvetoptimiser
  225. Sequencing NYC Subway bacteria????
  226. Downstream RNA-seq analysis without reference genome
  227. Minimum deep of coverage in a de novo transcriptome analysis
  228. Digital gene expression in CLC without reference genome
  229. Quick Evaluator of Denovo Assemblies
  230. velvetg ins_length parameter
  231. Coverage peak values meta-velvetg
  232. Does velvet assembler use RAM of all nodes altogether?
  233. How to predicate miRNA target without a reference genome
  234. Help with SGA
  235. BWA alignment using de novo velvet contigs
  236. Velvet lengyh k-mers
  237. Denovo assembly combine Ilumina PE reads and sanger reads
  238. Does velvet generate different assemblies from the same input data and same velvet pa
  239. Assembly annotation tool?
  240. Assembly with a single library always fail?
  241. Output unassembled reads from de novo assembly
  242. De Novo Transcriptome Assembly from Kmers only
  243. Abyss merge multiple assemblies
  244. Pipeline suggestions for gene detection
  245. Singletons, unique genes... outputs from velvet
  246. Adapter removal...
  247. Method for targeted sequencing
  248. Velvet 1.2.10: why the big difference in results with -long vs -short w/ 250bp reads?
  249. 2 strains.De novo or resequencing?
  250. Hybrid strategy? Got IonProton - which MiSeq?