{"id":693,"date":"2026-06-16T10:59:29","date_gmt":"2026-06-16T02:59:29","guid":{"rendered":"https:\/\/www.kz-hub.tech\/?p=693"},"modified":"2026-06-22T08:52:51","modified_gmt":"2026-06-22T00:52:51","slug":"%e4%bd%bf%e7%94%a8ampliconsuite-pipeline%e8%bf%9b%e8%a1%8cecdna%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"https:\/\/www.kz-hub.tech\/index.php\/2026\/06\/16\/%e4%bd%bf%e7%94%a8ampliconsuite-pipeline%e8%bf%9b%e8%a1%8cecdna%e5%88%86%e6%9e%90\/","title":{"rendered":"\u4f7f\u7528AmpliconSuite-pipeline\u8fdb\u884cecDNA\u5206\u6790"},"content":{"rendered":"

\u5b98\u65b9github\u7f51\u5740\uff1ahttps:\/\/github.com\/AmpliconSuite\/AmpliconSuite-pipeline<\/a>
\n\u7533\u8bf7mosek\u4e2a\u4eba\u514d\u8d39\u5b66\u672f\u8bb8\u53ef\uff1ahttps:\/\/www.mosek.com\/products\/academic-licenses\/<\/a>
\n\u7533\u8bf7\u540e\u653e\u5728~\/mosek\/\u4e0b<\/p>\n

1. \u4ecb\u7ecd<\/h2>\n

Focal oncogene amplification and rearrangements drive tumor growth and evolution in multiple cancer types. Proposed mechanisms for focal amplification include extrachromosomal DNA (ecDNA) formation, breakage-fusion-bridge (BFB) mechanism, tandem duplications, chromothripsis and others. Focally amplified regions are often hotspots for genomic rearrangements. As a result, the focally amplified region may undergo rapid copy number changes and the structure of the focally amplified region may evolve over time contributing to tumor evolution. Furthermore, ecDNA elements may reintegrate back into the genome to form HSRs. The inter-cell heterogeneity in copy number of ecDNA as well as the interchangeability between ecDNA and HSR may allow the tumor to adapt to changing environment, e.g. targetted drug application. As a result, understanding the architecture of the focal amplifications is important to gain insights into cancer biology. AmpliconArchitect (AA) is a tool which can reconstruct the structure of focally amplified regions (>10kbp) in a cancer sample using whole genome sequence short paired-end data.<\/p>\n

2. \u5b89\u88c5\u6d41\u7a0b\uff1a<\/h2>\n
conda create -n ampsuite && conda activate ampsuite\nconda install -c bioconda -c conda-forge ampliconsuite \nconda install -c mosek mosek\n\n# then run the installer script to finalize the locations of the data repo and mosek license \nwget https:\/\/raw.githubusercontent.com\/AmpliconSuite\/AmpliconSuite-pipeline\/master\/install.sh\nchmod +x install.sh\n.\/install.sh --finalize_only  # -h to see options<\/code><\/pre>\n
\u989d\u5916\u81ea\u884c\u4e0b\u8f7d\u6570\u636e\u5e93: https:\/\/refs.ampliconrepository.org\/?prefix=data\/module_support_files\/AmpliconArchitect\/<\/a>
\n\u5df2\u7ecf\u7ecf\u8fc7bwa\u6bd4\u5bf9\uff0c\u4e0b\u8f7d\u6ca1\u6709index\u7684GRCh38.tar.gz\u5373\u53ef<\/p>\n
3. \u5e76\u884c\u811a\u672c\uff1a<\/h2>\n
AA_DATA_REPO=~\/database\/AmpliconArchitect_repo\/\n\nperl -ne 'chomp; next if \/^$\/; @a = split \/\\t\/; print "AmpliconSuite-pipeline.py -s $a[0] -t 4 --normal_bam ..\/align\/$a[1]_bqsr.bam --bam ..\/align\/$a[0]_bqsr.bam --run_AA --run_AC > log\/$a[0].log 2>&1 && echo $a[0] AmpliconSuite ok\\n";' ..\/mutect2\/sample_pair.txt > RunAmpliconSuite.sh\n\n# \u8f93\u51fa\u793a\u4f8b\uff1aAmpliconSuite-pipeline.py -s FETB06-BLPT-E -t 4 --normal_bam ..\/align\/FETB06-N_bqsr.bam --bam ..\/align\/FETB06-BLPT-E_bqsr.bam --run_AA --run_AC > log\/FETB06-BLPT-E.log 2>&1 && echo FETB06-BLPT-E AmpliconSuite ok\n\nnohup bash -c "cat RunAmpliconSuite.sh | parallel -j 4" > log\/AmpliconSuite.log 2>&1 &<\/code><\/pre>\n
4. \u8f93\u51fa\u7ed3\u679c\u89e3\u8bfb:<\/h2>\n
AmpliconArchitect \u6700\u7ec8\u8f93\u51fa\u7ed3\u679c\u4e3a\uff1aSAMPLE_AA_results\/SAMPLE_summary.txt\uff0c\u5176\u4e2d\u5305\u542b\u4e86\u201c\u5c40\u90e8\u6269\u589e\u533a\u57df\u201d<\/p>\n
#Amplicons = 8\n-----------------------------------------------------------------------------------------\n[amplicon1] AmpliconID = 1\n[amplicon1] #Intervals = 1\n[amplicon1] Intervals = chr2:94499495-94573455\n[amplicon1] OncogenesAmplified = ,\n[amplicon1] TotalIntervalSize = 73961\n[amplicon1] AmplifiedIntervalSize = 73960\n[amplicon1] AverageAmplifiedCopyCount = 6.88546257606703\n[amplicon1] #Chromosomes = 1\n[amplicon1] #SequenceEdges = 1\n[amplicon1] #BreakpointEdges = 0\n[amplicon1] #CoverageShifts = 0\n[amplicon1] #MeanshiftSegmentsCopyCount>5 = 0\n[amplicon1] #Foldbacks = 0\n[amplicon1] #CoverageShiftsWithBreakpointEdges = 0\n[amplicon1] #TotalAmpliconWeight = 509255.698\n[amplicon1] #FractionWeightInDecomp = 1.00000000\n[amplicon1] -----------------------------------------------------------------------------------------\n[amplicon2] AmpliconID = 2\n[amplicon2] #Intervals = 1\n[amplicon2] Intervals = chr3:90315297-90505827\n[amplicon2] OncogenesAmplified = ,\n[amplicon2] TotalIntervalSize = 190531\n[amplicon2] AmplifiedIntervalSize = 190528\n[amplicon2] AverageAmplifiedCopyCount = 5.204942372970038\n[amplicon2] #Chromosomes = 1\n[amplicon2] #SequenceEdges = 3\n[amplicon2] #BreakpointEdges = 1\n[amplicon2] #CoverageShifts = 0\n[amplicon2] #MeanshiftSegmentsCopyCount>5 = 0\n[amplicon2] #Foldbacks = 0\n[amplicon2] #CoverageShiftsWithBreakpointEdges = 0\n[amplicon2] #TotalAmpliconWeight = 991702.875\n[amplicon2] #FractionWeightInDecomp = 1.00001048\n[amplicon2] -----------------------------------------------------------------------------------------<\/code><\/pre>\n
AmpliconClassifier \u6700\u7ec8\u8f93\u51fa\u7ed3\u679c\u4e3a\uff1a<\/p>\n
    \n
  1. SAMPLE_amplicon_classification_profiles.tsv<\/li>\n
  2. SAMPLE_gene_list.tsv<\/li>\n
  3. SAMPLE_ecDNA_context_calls.tsv<\/li>\n<\/ol>\n
    SAMPLE_amplicon_classification_profiles.tsv:<\/p>\n
    sample_name     amplicon_number amplicon_decomposition_class    ecDNA+  BFB+    ecDNA_amplicons\nFETB06-BLPT-M   amplicon1       Linear  None detected   None detected   0\nFETB06-BLPT-M   amplicon2       Linear  None detected   None detected   0\nFETB06-BLPT-M   amplicon3       Linear  None detected   None detected   0\nFETB06-BLPT-M   amplicon4       Complex-non-cyclic      None detected   None detected   0\nFETB06-BLPT-M   amplicon5       Linear  None detected   None detected   0\nFETB06-BLPT-M   amplicon6       Linear  None detected   None detected   0\nFETB06-BLPT-M   amplicon7       Linear  None detected   None detected   0\nFETB06-BLPT-M   amplicon8       Linear  None detected   None detected   0<\/code><\/pre>\n
    \u5408\u5e76\u6587\u4ef6\uff1a<\/p>\n
    find . -path '.\/*_classification\/*_amplicon_classification_profiles.tsv' \\\n  | sort \\\n  | xargs awk '\nFNR==1 {\n    if (NR==1) print $0\n    next\n}\n{\n    print $0\n}\n' > All_amplicon_classification_profiles.tsv<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"
    \u5b98\u65b9github\u7f51\u5740\uff1ahttps:\/\/github.com\/AmpliconSuite\/AmpliconSui…<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3],"tags":[],"class_list":["post-693","post","type-post","status-publish","format-standard","hentry","category-3"],"_links":{"self":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/693","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/comments?post=693"}],"version-history":[{"count":4,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/693\/revisions"}],"predecessor-version":[{"id":704,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/693\/revisions\/704"}],"wp:attachment":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/media?parent=693"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/categories?post=693"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/tags?post=693"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}