Frequently Used: User Manuals, Guides, Tutorials

Manuals

  1. ASReml user guides (version 2 | version 3)
  2. ABYSS
  3. Biomart User Manual
  4. BEDOPS - scalable genome analysis toolkit
  5. BEDTools
  6. Blat: Program Specifications and User Guide
  7. Blast: program options and helps
  8. Blast+ (new): User manual
  9. Bowtie (Manual | Tutorial)
  10. BRAT
  11. Blastz: genome sequence alignment
  12. BWA { BWA Tutorials: 1, 2, man page }
  13. CAP3 (General helps | Assembly | Improved)
  14. Carthagene
  15. Cistematic
  16. Clustalw: README
  17. CRI-MAP (Doc | Home | Tutorial)
  18. ContigImage
  19. e-PCR | me-PCR
  20. Exonerate
  21. fastPHASE (Abstract)
  22. HISAT2
  23. Long Horn Array DB
  24. MEGAN
  25. map2GO_slim
  26. Gmap-gsnap
  27. miranda - find miRNA sites
  28. MPIblast
  29. PHASE ( web, FAQ, etc.)
  30. Otterlace ( Guidelines | User Manual )
  31. Oases
  32. Primer3: README
  33. PLINK
  34. PLINK/SEQ
  35. RepeatMasker
  36. R
  37. REPCLASS (cluster computer)
  38. RTG
  39. RepeatScout (cluster computer)
  40. RHmapper
  41. SamTools (BCF/VCF | Bowtie | Source)
  42. seqtk
  43. SnpEff
  44. Shore
  45. Sibs: README
  46. SOAPdenovo
  47. SRA Tool kit (NCBI)
  48. Tophat
  49. Tophat-fusion
  50. Variant Effect Predictor (Source | Tutorial)
  51. VCF Tools
  52. Velvet
  53. WU-Blast: Topics
  54. XPLCR

Tutorials

  1. BioPerl
  2. Crimap (an anatomy | a tour)
  3. OMIM
  4. GBrowse Tutorials
  5. DNA Sequence Analysis: GCG
  6. DNA Sequence Analysis: Staden
  7. Seq Data Mapping Tutorial
  8. Merlin: Pedigree/linkage analysis
  9. Plink: Whole genome association analysis

Decode Illumina Strands

File formats

Links

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