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• is-1808131641-reassemble-gaps
• add-missing-threads-param-to-blastn
• add-sambamba
• add-yapf-style
• al-add-indices
• al-fix-xGen-indices
• al-illumina-indices_180325
• blastn_numthreads
• bump-baseimage
• bump-snakemake-version
• change_argparse_help_format
• cleanup-config_yaml
• conda-fix
• conda-tool-install-changes
• conda-update-support
• ct-1.25.0_kraken_hotfix
• ct-add-alignment-stats
• ct-add-barcode-frequency-list
• ct-add-bwa-depletion
• ct-add-clumpify
• ct-add-conda-gatk
• ct-add-conda-recipe
• ct-add-coverage-plot
• ct-add-developer-docs
• ct-add-dockerfile
• ct-add-downsampling-tool
• ct-add-dp-pipeline-diagram
• ct-add-fastq-to-bam
• ct-add-flowcell-types
• ct-add-git-to-dockerignore
• ct-add-mafft
• ct-add-matplotlib-to-docs-requirements
• ct-add-merge-to-vcf
• ct-add-post-checkout-env-update-hook
• ct-add-pseudoversion-sans-git
• ct-add-tarball-merger
• ct-add-travis-slack-integration
• ct-additional-demux-launcher-inputs
• ct-adjust-version-detection
• ct-ag100-exploration
• ct-aggregate-spike-counts
• ct-align-and-fix-unmarked-option
• ct-align_and_plot_wdl_tar
• ct-allow-runinfo-demux-override
• ct-alter-reports-only
• ct-arg-cast
• ct-bam-sort-check
• ct-barcodes-speedup
• ct-base-curl
• ct-breakout-snake-tests
• ct-broad-cluster-mem-change
• ct-broad-uger-core-bindings
• ct-broad_uger_runtime_changes
• ct-bugfix-accession-list-newer-snakemake
• ct-bugfix-align-and-plot-bam-deletion
• ct-bugfix-ncbi-annotation
• ct-bugfix-samplesheet-csv
• ct-bugfix-snakemake-pipeline
• ct-bugfix-snpeff
• ct-bugfix-taxon_filter-parser
• ct-bugfix-wdl-merge_bams
• ct-build-docker
• ct-build-fix
• ct-build-fixes
• ct-build-fixes2
• ct-build-stages
• ct-bump-cromwell-and-dx
• ct-bump-picard
• ct-bump-pysam
• ct-bump-pysam-samtools
• ct-bump-pytest
• ct-bump-tbl2asn
• ct-bump-viral-baseimage
• ct-bwa-deplete-db-snakemake
• ct-bwa-deplete-unpaired-tolerant
• ct-catch-snpEff-failure
• ct-change-travis-shallow-clone-depth
• ct-chunk-lastal
• ct-cluster-mem-adjust
• ct-code-qc
• ct-collect-illumina-lane-metrics
• ct-common-barcodes-and-other-fixes
• ct-conda-build-bump
• ct-conda-build-debug
• ct-conda-channel-order
• ct-conda-corrections
• ct-conda-forge-depend
• ct-conda-install-change
• ct-conda-package-version-comparison-patch
• ct-conda-post-verify-command
• ct-conda-update-always
• ct-conda-updates
• ct-condafy-easy-deploy-broad
• ct-condafy-tbl2asn
• ct-condafy-tools
• ct-condafy-tools-travis-debug
• ct-condafy-travis-debug
• ct-correct-trinity-version-string
• ct-coverage-plot-bugfix
• ct-coverage-plot-dupe-options
• ct-db-path-lists
• ct-debug-bwa-deplete
• ct-debug-feature-table
• ct-debug-novaseq-demux
• ct-debug_demux
• ct-demux
• ct-demux-changes-for-nextseq
• ct-demux-debug
• ct-demux-wdl-bugfix
• ct-demux-wdl-pass-runinfo
• ct-demux-zero-mismatches-allowed
• ct-demux_launcher-input-correction
• ct-depletion-revert-read-tags
• ct-diamond-fix
• ct-dnanexus-mention-latest
• ct-do-not-upload-dev-conda-pkg
• ct-do-not-upload-dev-conda-pkgs
• ct-docker-multi-login
• ct-dockerhub-for-wdl
• ct-docs
• ct-docs-build
• ct-docs-update
• ct-downgrade-matplotlib
• ct-downsample-wdl-correction
• ct-downsample-wdl-debug
• ct-drop-py27
• ct-dsub-docs
• ct-dx-demux-novaseq-debug
• ct-easy-deploy
• ct-easy-deploy-changes
• ct-easy-deploy-correction
• ct-easy-deploy-pathlength-fix
• ct-easy-deploy-ram-check
• ct-easy-deploy-update
• ct-empty-barcodes
• ct-enable-osx-builds
• ct-explicit-conda-channels
• ct-expoe-novoalign-param-strings
• ct-expose-params
• ct-expose-ref-guided-consensus-novo-params
• ct-expose-scaffolding-option-in-config
• ct-extend-align-and-plot-coverage
• ct-feature-clip-annotation-change
• ct-feature-clipping-fix
• ct-feature-table-id-parser
• ct-featuretable-solo-qualifier-key
• ct-filename-escapes
• ct-filter-bam
• ct-filter-out-reads-beginning-with-indel
• ct-fix-bwamem_idxstats
• ct-fix-demux-checkdir
• ct-fix-pylintrc
• ct-fix-snakemake-params
• ct-fix-trimmomatic
• ct-flagstat-primary-alignments-only
• ct-flowcells-config-comment
• ct-formatting
• ct-gatk-docs-link-update
• ct-gatk-wdl-locate
• ct-gatk3-exec-fallback
• ct-guess-barcodes
• ct-gzip-to-pigz
• ct-handle-tbl2asn-oddness
• ct-harden-samplesheet-input
• ct-hiseq4k_x_demux_hardening
• ct-illumina-adapters
• ct-illumina-index-ref
• ct-illumina-single-index-barcode-count
• ct-illumina-single-sample
• ct-increase-trinity-mem
• ct-increase-uger-mem
• ct-install-badge
• ct-install-conda-pkgs-to-separate-env-in-Docker
• ct-intrahost-changes-from-alin
• ct-kraken-memory-correction
• ct-kraken-wdl-viral-summary
• ct-krakenuniq-summary-kmer-filter
• ct-landscape-changes
• ct-landscape-improvements
• ct-lastal-filter-qc-check
• ct-log-output-corrections
• ct-maf-convert-explicit-interpreter
• ct-max-threads-picard
• ct-merge-tarballs-wdl
• ct-metag-summary-error-reporting
• ct-metagenomic-report-merger
• ct-misc-fixes
• ct-mlin-demux-launcher
• ct-mock-bioseqrecord
• ct-mock-matplotlibpyplot-for-docs
• ct-mosaik-dynamic-linking
• ct-multialign
• ct-multialign-annotation-transfer-oob-fix
• ct-multialign-dev
• ct-multialign-dev2
• ct-multialign-snpeff-db-build
• ct-note-pytest-tool-install-in-docs
• ct-omit-conda-build
• ct-option-to-pass-in-gatk
• ct-orient-impute-corrections
• ct-osx-travis-changes
• ct-output-version-in-wdls
• ct-parallel-lastal
• ct-parallelize-blastn-calls
• ct-pass-jvmmemory
• ct-patch-uger-jobscript
• ct-pin-attrs
• ct-pin-conda-bugfix
• ct-pin-snakemake
• ct-pin-tbl2asn
• ct-plot-bugfix
• ct-plot-with-sample-name-title
• ct-post-conda-cmd
• ct-preserve-ercc-in-spikein-report
• ct-py27-test-fixes
• ct-py35-test
• ct-pylint-improvements
• ct-re-condafy-tools
• ct-refactor-a-few-things
• ct-refactor-common-barcodes
• ct-refactor-easy-deploy-broad
• ct-refine-assembly-robust-to-empty-input
• ct-reformat-docker-docs
• ct-remote-db-bugfixing
• ct-remote-trigger-revision
• ct-remove-ansible-config
• ct-remove-debug
• ct-remove-deploy-files
• ct-remove-docker-travis-wait
• ct-remove-kraken-custom-installers
• ct-remove-stale-symlink
• ct-remove-uger-proj
• ct-remove-yappi
• ct-rename-easy-deploy
• ct-rename-easy-deploy-script
• ct-rename-task-wdls
• ct-repair-malformed-zip
• ct-restore-unmatched-bam-wdl
• ct-retry-conda-install
• ct-retry-travis-conda-install
• ct-revert-bam-bugfix
• ct-revert-mosaik-avoid-buffer-overflow
• ct-revertsam-only-if-aligned
• ct-revise-install-instructions
• ct-revise-reports_only
• ct-revisit-run-and-print
• ct-rework-trinity-prep
• ct-run-pipe-from-conda
• ct-samplesheet-parse
• ct-samplesheet-parse-fix
• ct-samplesheet-remove-bom
• ct-samplesheet-txt-tabfile
• ct-samtofastq-rmdup-corrections
• ct-samtools-view-threads
• ct-scaffold-changes
• ct-scale-lastal-ram
• ct-separate-taxlevel-summary-task
• ct-single-end-bwa-deplete
• ct-skip-genbank-tests
• ct-snakemake-db-refactor
• ct-snakemake-notemp
• ct-snakemake-txt-skip-blank-lines
• ct-sort-wdl-spikein-report
• ct-spikein-aggregator-loglevel-patch
• ct-stub-out-doubly-mapped-failure-mode
• ct-subparser-help
• ct-subsample-bam-space
• ct-tabixfile-comment
• ct-tag-cache-du-fix
• ct-testing-metag-pipe-fixes
• ct-tmp-fix-for-uger
• ct-toggle-tests
• ct-travis-changes
• ct-travis-conda-debug2
• ct-travis-retry-conda-install
• ct-travis-ubuntu14.04
• ct-trigger-other-repo
• ct-trigger-script-change
• ct-trimmomatic-cutoff-values
• ct-trinity-in-same-conda-env
• ct-trinity-prep-clipping
• ct-try-signing
• ct-try-wdl
• ct-typo-fix
• ct-uger-bugfixes
• ct-uger-spec
• ct-unset-java-home
• ct-update-baseimage
• ct-update-blast
• ct-update-conda-packge-regex
• ct-update-deps
• ct-update-diamond
• ct-update-docs
• ct-update-docs-and-easy-deploy
• ct-update-docs-deps
• ct-update-docs-for-conda
• ct-update-docs-for-hosted-dbs
• ct-update-docs-gatk
• ct-update-docs-krakendb
• ct-update-docs-mention-contaminants
• ct-update-dxwdl
• ct-update-easy-deploy
• ct-update-easy-install
• ct-update-easy-install-docs
• ct-update-fastqc
• ct-update-gatk-source-url
• ct-update-java-on-travis
• ct-update-krona
• ct-update-licensed-tools
• ct-update-matplotlib
• ct-update-mosaik
• ct-update-novoalign
• ct-update-novoalign-3_07_00
• ct-update-novoalign-path
• ct-update-novoalign-version
• ct-update-perl
• ct-update-picard
• ct-update-picard-2.20.3
• ct-update-picard-2_21_1
• ct-update-picard-jul18
• ct-update-pipe-scripts
• ct-update-pysam
• ct-update-pytest
• ct-update-pyyaml
• ct-update-reports-rules
• ct-update-rundocker
• ct-update-snake-docs
• ct-update-snakemake
• ct-update-snakemake-docs
• ct-update-snakemake-resources
• ct-update-spikein-reference
• ct-update-travis
• ct-update-trimmomatic
• ct-update-viral-baseimage
• ct-update-wdl-ercc-default
• ct-use-active-conda-env
• ct-various-corrections
• ct-various-fixes
• ct-vcf_merge_naive_filter-correction
• ct-vphaser-wdl
• ct-wdl-aggregate-spikein-reports
• ct-wdl-debug
• ct-wdl-demux
• ct-wdl-metag-fix
• ct-wdl-skip-mark-dupes
• ct-wdl-task-update
• ct-wdl-type-fix
• ct_illumina_indices_typofix
• ct_md5_assert_fail_msg
• docs-typo-fix
• dp-89-isnv-merge
• dp-add-make
• dp-align
• dp-align-orient
• dp-align-to-ref
• dp-alt-contigs
• dp-annot
• dp-annot-fix
• dp-badges
• dp-bmtagger
• dp-build
• dp-build-d
• dp-build-optim
• dp-bwa
• dp-cmapper
• dp-conda
• dp-cromwell
• dp-dem
• dp-demux
• dp-dev
• dp-diamond-debug
• dp-distutils
• dp-docker
• dp-docker-tweaks
• dp-docs
• dp-dx
• dp-dx-fix
• dp-dx-update
• dp-dxwdl
• dp-empty-data
• dp-fix
• dp-fix-bmtaggerx
• dp-fix-conda
• dp-fix-flagstat
• dp-fix-ill
• dp-fix-novoalign-ntfs
• dp-fix-run-and
• dp-fix-tool-patch
• dp-gaps
• dp-gatk4
• dp-genbank
• dp-indels
• dp-isnv-fix
• dp-kraken
• dp-kraken-osx
• dp-kraken-pipe
• dp-kraken2
• dp-krona
• dp-lastal
• dp-lastal-simple
• dp-libstats
• dp-merge-bams
• dp-merge-fix
• dp-meta-docs
• dp-mummer
• dp-mummer-params
• dp-mummer-sensitivity
• dp-nigeria
• dp-no_samtools
• dp-novogatk
• dp-novoindex
• dp-one-barcode
• dp-osx
• dp-picard
• dp-pretrinity
• dp-pysam081
• dp-readme
• dp-report-raw-count
• dp-reports
• dp-requirements
• dp-samplesheet
• dp-scaffold
• dp-scaffold-logging
• dp-spikeins
• dp-test-km
• dp-test_trinity
• dp-threads
• dp-travis-cache
• dp-trinity
• dp-trinity-341
• dp-trinity-conda-fix
• dp-uger-fix
• dp-uger-job
• dp-undef-fix
• dp-unpaired
• dp-updates
• dp-wdl
• dp-workflows
• dpark-depletion-pipeline
• dpark-dev
• dpark-fix-pipes
• dpark-snpeff
• dpark-tools
• easy-deploy-broad
• easy-deploy-run-relative-fix
• enable-osx-builds
• escape-sample-names
• fix-novo-rgs
• fix-reports-glob
• fix-trimmomatic-bug
• genbank-prep-multisegment-support
• hm-add-bwa-score-filter
• hm-add-covg-plot-axis-limits
• hm-add-kraken-rule
• hm-add-read-count-to-vcf
• hm-blacklist-sgi1
• hm-blacklist-uger-nodes
• hm-cleanup-krona-tmp-files
• hm-dont-require-gi-map
• hm-fix-bwa-aln
• hm-fix-depletion-threads
• hm-fix-interhost-rules
• hm-fix-json-serializability-bug
• hm-fix-merge-one-per-sample-inputs
• hm-fix-metagenomics-input
• hm-fix-nonoverlapping-seqs
• hm-fix-plot-covg-missing-bam
• hm-fix-reports
• hm-fix-reports-with-no-coverage
• hm-fix-sample-id-regex
• hm-fix-spikein-align
• hm-muv-downsampled-assembly
• hm-zikv
• hm-zikv-changes
• hml-80-complete
• hml-80-complete_irwin_merged
• hml-blast
• hml-bwa
• hml-samtools
• hybsel-analysis
• improve-conda-logging
• irwin-3MinorChanges
• irwin-CoordMapper
• irwin-DownloadScript
• irwin-betterCoordMapper
• irwin-binaries
• irwin-blastn
• irwin-bmtagger
• irwin-bmtaggerBug
• irwin-bmtaggerURL
• irwin-fix_test_taxon_filter
• irwin-fixes
• irwin-iSNVstep1
• irwin-isnv-merge
• irwin-issue12
• irwin-issue20
• irwin-lastl
• irwin-libBias
• irwin-math
• irwin-mvicuna
• irwin-path-cleanups
• irwin-sandbox
• irwin-split
• irwin-stats
• irwin-taxon_filter
• irwin-taxon_filter_interfaces
• irwin-testingbug
• irwin-tool_enhancements
• irwin-trimmomatic
• irwin-vphaser
• irwin_fixTestFastqBam
• irwin_mosaik
• is-180806-b4-rewrite-master
• is-180806-misc-fixes-01
• is-180806-update-spades-to-3.12.0
• is-1808062244-improve-spades
• is-1808081312-add-bbmap
• is-1808081327-add-abyss
• is-1808131307-exper0818
• is-1808201231-add-finishing
• is-1808231208-update-novoalign-to-3.09
• is-1808241104-refine-assembly-add-reporting
• is-1808251951-test-git-annex
• is-1808252024-add-benchmarks
• is-1808252024-add-benchmarks--01-clean-impl
• is-1808252024-add-benchmarks--02-make-dx-import-work
• is-1808252024-add-benchmarks-add-cromwell-on-aws-batch
• is-add-asm-improvability-metrics
• is-add-asm-improvability-metrics-b/wip-generic-asm-stage-reports
• is-add-assembly-optimality-reports
• is-add-benchmarks-crogit-wip-03
• is-add-benchmarks-imp-dx
• is-add-check-paths
• is-add-gap2seq
• is-add-gapfill-to-pipeline
• is-add-kmc
• is-add-metaspades
• is-add-metaspades-and-fix-mummer-scaffolding
• is-add-protein-taxon-filt
• is-add-read-utils
• is-add-sealer
• is-add-spades
• is-assembly-eval
• is-better-handle-misassemblies
• is-bump-baseimage-to-0.1.14
• is-bump-coveralls-to-1.3
• is-ci-add-dx-timeouts
• is-cms2
• is-config-include
• is-drop-ambig-aligns
• is-dummy-checkin
• is-dx-benchmarks
• is-faster-tests
• is-finishing
• is-fix-assembly-wdl
• is-fix-assembly-wdl-new
• is-fix-ci-ostype
• is-fix-conda-channel-order-and-min-reqs
• is-fix-config
• is-fix-conftest
• is-fix-docker-mem
• is-fix-gatk-3.8
• is-fix-gatk-mindepth
• is-fix-illumina-missing-files-handling
• is-fix-kraken
• is-fix-master-history
• is-fix-tempfile-issue
• is-fix-test-cromwell
• is-fix-test-tempfiles
• is-fix-wdl-assemble-trinity-spades
• is-fix-wdl-type-bug
• is-fixing-cpu-count
• is-keeptmp
• is-kmer-cov
• is-metadata
• is-metadata-recording
• is-metadata-recording-1
• is-modularize-assembly
• is-mrg-all
• is-mult-refs
• is-mummer-use-show-coords
• is-new-add-utils
• is-new-fix-cromwell-local-tests
• is-new-mrg-all
• is-new-use-closest-reference
• is-pytest-fixes
• is-readd-gapfill-to-pipeline
• is-reference-selection
• is-refsel-handle-failures
• is-restore-redundant-testing
• is-scaffold-with-misassemblies
• is-simpler-config
• is-spades-2
• is-spades-add-always-succeed
• is-spades-min-contig-len
• is-spades-sep-libs
• is-split-ci
• is-tag-b4-merge-config-includes
• is-test-master
• is-test-master-01
• is-test-master-2
• is-test-null-change
• is-update-pytest-to-4.0.2
• is-update-spades-to-3.12.0
• is-update-spades-to-3.13.0
• is-update-spades-to-3.13.0-new
• is-use-closest-reference
• is-use-kmc
• isnv-test-data
• json-to-yaml
• large_files_md5
• lk-binned-coverage-plots
• lk-bulk_assemble_denovo
• master
• minor-mafft-fix
• mlin-dx-launcher
• mlin-dx-launcher-consolidate
• origin/hm-fix-metagenomics-input
• relocate-conda-cache
• remove-tango
• restyle-log
• revert-936-sy-remove-merge-compressed
• run-pipe-config-file-revert
• run-pipe-corrections
• run-pipe-improvements
• run_and_print_check
• single-end-improvements
• small-pylint-fixes
• sort_vphaser_input
• staging
• sy-advance-reservation
• sy-align-nosensitive
• sy-align-rna-36
• sy-bash-pipes
• sy-blast-lca
• sy-bump-kraken
• sy-bwa-metagenomics
• sy-cdd
• sy-cdhit
• sy-cleaned-metagenomics
• sy-conda-overwrite-env
• sy-conda-python
• sy-conda-speedup
• sy-conda-v-warning
• sy-conda4
• sy-condastub
• sy-coverage-nomoduleimport
• sy-coverage-subprocess
• sy-covlca-parents
• sy-diamond-env
• sy-diamond-integration
• sy-diamond-leftover
• sy-diamond-newtax
• sy-diamond-pipes
• sy-diamond-tax
• sy-diamond-update
• sy-dupes-swap
• sy-faster-kraken-tests
• sy-fixture-durations
• sy-fixtures-kraken
• sy-gatk-conda-reqs
• sy-increase-dedup-memory
• sy-indicate-jobid
• sy-integration-kraken
• sy-java-version
• sy-jobid-tab
• sy-jobscript-resources
• sy-join-y
• sy-kraken-db-diveristy
• sy-kraken-multiple
• sy-kraken-no-prepend
• sy-kraken-pipes
• sy-kraken-rule-tweak
• sy-kraken-single-default
• sy-kraken-tests-refactor
• sy-kraken-viral-mix-test
• sy-kraken2-deplete
• sy-krakenuniq
• sy-krakenuniq-dev
• sy-krona-db
• sy-krona-integration
• sy-krona-kmers
• sy-krona-skip
• sy-large-files-md5
• sy-lca-scan
• sy-merge-exception
• sy-merge-one-queue
• sy-meta-align-fixes
• sy-metabwa-update
• sy-metagenomics-fixes
• sy-metagenomics-krona
• sy-metagenomics-rules
• sy-metagenomics-unit-tests
• sy-metagenomics-work
• sy-more-tool-checks
• sy-ncbitax
• sy-no-immediate
• sy-nodupes
• sy-optional-spikein
• sy-pip-cache
• sy-pipes-tmp
• sy-pr-long-tests
• sy-py3
• sy-pysam-update
• sy-pytest
• sy-pytest-logging
• sy-pytest-requirements
• sy-pytest-session-tmpdir
• sy-pytest-update
• sy-quiet-conda
• sy-remove-merge-compressed
• sy-remove-tox
• sy-requirements-hooks
• sy-run-and-print-fix
• sy-run-and-print-fixes
• sy-run-check
• sy-runpipe-echo
• sy-smaller-tests
• sy-snakeremote
• sy-subprocess-run
• sy-taxon-filter-updates
• sy-tooling-misc
• sy-trinity-conda-env
• sy-trinity-ulimit
• sy-typos
• sy-unitify-test-tools-kraken
• sy-update-picard
• sy-update-pytest
• sy-update-tox
• sy-use-uger
• sy-whitespace-cleanup
• sy-yapf
• sy-zst
• synced/is-1808251951-test-git-annex
• synced/is-1808252024-add-benchmarks
• tbl2asn-version-fix
• test_deplete_human
• tomkinsc-patch-1
• travis-py27
• update-docs
• update-prinseq
• v0.2.0
• v0.2.2
• v0.2.3
• v0.2.4
• v0.3.0
• v0.3.1
• v0.3.2
• v0.3.3
• v0.3.4
• v0.4.0
• v0.5.0
• v0.5.1
• v0.5.2
• v0.5.3
• v0.5.4
• v0.5.5
• v0.9.0
• v0.9.1
• v1.0.0
• v1.1.0
• v1.1.1
• v1.1.2
• v1.1.3
• v1.10.0
• v1.10.1
• v1.11.0
• v1.12.0
• v1.12.1
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• v1.13.2
• v1.13.3
• v1.13.4
• v1.14.0
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• v1.15.1
• v1.15.2
• v1.15.3
• v1.15.4
• v1.16.0
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• v1.17.1
• v1.17.2
• v1.17.3
• v1.18.0
• v1.18.1
• v1.18.2
• v1.19.0
• v1.19.1
• v1.19.2
• v1.19.3
• v1.2.0
• v1.2.1
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• v1.8.0
• v1.9.0
• v1.9.1
• v1.9.2
• variable-ec2-region-for-easy-deploy

Changed reference selection to maximize the number of well-covered
kmers after imputing the scaffold with each reference.
Added option of outputting imputed scaffold with each reference.