sequenceassemblymanager-文庫吧
2025-09-08 15:02 本頁面
【正文】 tegral part of the system XML makes system generic and flexible Trace Archive Data XML File Sample ?xml version= ? trace_volume volume_nametrace archive/volume_name volume_dateFri Aug 15 15:04:26 PDT 2020/volume_date volume_versionvolume_version / trace trace_name/trace_name trace_directory/home/sequence/Projects/Rhodococcus_RHA1/Assemblies/Repository/trace_directory center_nameBCGSC/center_name center_projectRhodococcus RHA1/center_project library_idRT005/library_id plate_number1/plate_number plate_quadrantb/plate_quadrant clone_idRT0051bA01/clone_id template_idRT0051bA01/template_id insert_size34750/insert_size quality_length747/quality_length vector_quality30/vector_quality insert_stddev3600/insert_stddev well_idA01/well_id trace_sequencetgggggggtctggtacgaatttcttttcgtggacgctttcgcgtt…tctcccttgcgtttggagttgagtctttatt /trace_sequence trace_quality6 6 8 9 9 9 9 9 7 7 9 13 13… 9 9 9 9 9 7 7 9 8 8 8 8 13 6 6 8 6 6 10 8 8 6 6 8 6 6 9 8 6 6 6 /trace_quality trace_endU/trace_end run_date20200814 12:49:38/run_date typeunpaired_production/type trace_length1394/trace_length /trace trace … /trace … /trace_volume Sequence Assemblers Glimmer Arachne GeneMark Phrap Phrap ●Allows use of entire read (not just trimmed high quality part) ●Construct contig sequence as a mosaic of the highest quality parts of the reads Arachne ●Trims terminal regions of low quality and eliminate reads with overall low quality ● Eliminate duplicate reads(exact and highly similar) ●Build contigs by merging read pairs that don39。t cross a repeat boundary ●Supercontig creation by linking pairs of contigs sharing =2 forwardreverse links (2 clones) Concurrently use 2 public Assemblers: Phrap and Arachne System is designed to easily “Plug in” any new assemblers Proper wrapper must be written for each new added programs Sequence Assemblers Anatomy of WGS Sequence Assemblies F R Contigs Sequencing amp。 Trace processing Assembly Paired end reads Singleton Supercontigs: Higher Arrangements of Contigs (sequence gaps estimated and contigs oriented Supercontig
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鄂ICP備17016276號-1