CA8/Linux-amd64/bin/PBcR
CA8/Linux-amd64/bin/TIGR/AsmLib.pm
CA8/Linux-amd64/bin/TIGR/Foundation.pm
CA8/Linux-amd64/bin/addCNSToStore
CA8/Linux-amd64/bin/addReadsToUnitigs
CA8/Linux-amd64/bin/analyzeBest
CA8/Linux-amd64/bin/analyzePosMap
CA8/Linux-amd64/bin/analyzeScaffolds
CA8/Linux-amd64/bin/asmOutputFasta
CA8/Linux-amd64/bin/asmOutputStatistics
CA8/Linux-amd64/bin/asmToAGP.pl
CA8/Linux-amd64/bin/blasr
CA8/Linux-amd64/bin/bogart
CA8/Linux-amd64/bin/bogus
CA8/Linux-amd64/bin/bogusness
CA8/Linux-amd64/bin/buildPosMap
CA8/Linux-amd64/bin/buildRefContigs
CA8/Linux-amd64/bin/buildUnitigs
CA8/Linux-amd64/bin/ca2ace.pl
CA8/Linux-amd64/bin/caqc.pl
CA8/Linux-amd64/bin/caqc_help.ini
CA8/Linux-amd64/bin/cat-corrects
CA8/Linux-amd64/bin/cat-erates
CA8/Linux-amd64/bin/cgw
CA8/Linux-amd64/bin/cgwDump
CA8/Linux-amd64/bin/chimChe
CA8/Linux-amd64/bin/chimera
CA8/Linux-amd64/bin/classifyMates
CA8/Linux-amd64/bin/classifyMatesApply
CA8/Linux-amd64/bin/classifyMatesPairwise
CA8/Linux-amd64/bin/computeCoverageStat
CA8/Linux-amd64/bin/convert-fasta-to-v2.pl
CA8/Linux-amd64/bin/convertOverlap
CA8/Linux-amd64/bin/convertToPBCNS
CA8/Linux-amd64/bin/correct-frags
CA8/Linux-amd64/bin/correct-olaps
CA8/Linux-amd64/bin/correctPacBio
CA8/Linux-amd64/bin/ctgcns
CA8/Linux-amd64/bin/deduplicate
CA8/Linux-amd64/bin/demotePosMap
CA8/Linux-amd64/bin/dumpCloneMiddles
CA8/Linux-amd64/bin/dumpPBRLayoutStore
CA8/Linux-amd64/bin/dumpSingletons
CA8/Linux-amd64/bin/erate-estimate
CA8/Linux-amd64/bin/estimate-mer-threshold
CA8/Linux-amd64/bin/extendClearRanges
CA8/Linux-amd64/bin/extendClearRangesPartition
CA8/Linux-amd64/bin/extractmessages
CA8/Linux-amd64/bin/falcon_sense
CA8/Linux-amd64/bin/fast_consensus.pl
CA8/Linux-amd64/bin/fastaToCA
CA8/Linux-amd64/bin/fastqAnalyze
CA8/Linux-amd64/bin/fastqSample
CA8/Linux-amd64/bin/fastqSimulate
CA8/Linux-amd64/bin/fastqSimulate-sort
CA8/Linux-amd64/bin/fastqToCA
CA8/Linux-amd64/bin/filterOverlap
CA8/Linux-amd64/bin/finalTrim
CA8/Linux-amd64/bin/fixUnitigs
CA8/Linux-amd64/bin/fragmentDepth
CA8/Linux-amd64/bin/fragsInVars
CA8/Linux-amd64/bin/frgs2clones
CA8/Linux-amd64/bin/gatekeeper
CA8/Linux-amd64/bin/gatekeeperbench
CA8/Linux-amd64/bin/gkpStoreCreate
CA8/Linux-amd64/bin/gkpStoreDumpFASTQ
CA8/Linux-amd64/bin/greedyFragmentTiling
CA8/Linux-amd64/bin/greedy_layout_to_IUM
CA8/Linux-amd64/bin/initialTrim
CA8/Linux-amd64/bin/markRepeatUnique
CA8/Linux-amd64/bin/markUniqueUnique
CA8/Linux-amd64/bin/merTrim
CA8/Linux-amd64/bin/merTrimApply
CA8/Linux-amd64/bin/mercy
CA8/Linux-amd64/bin/mergeqc.pl
CA8/Linux-amd64/bin/meryl
CA8/Linux-amd64/bin/metagenomics_ovl_analyses
CA8/Linux-amd64/bin/olap-from-seeds
CA8/Linux-amd64/bin/outputLayout
CA8/Linux-amd64/bin/overlapInCore
CA8/Linux-amd64/bin/overlapStats
CA8/Linux-amd64/bin/overlapStore
CA8/Linux-amd64/bin/overlapStoreBucketizer
CA8/Linux-amd64/bin/overlapStoreBuild
CA8/Linux-amd64/bin/overlapStoreIndexer
CA8/Linux-amd64/bin/overlapStoreSorter
CA8/Linux-amd64/bin/overlap_partition
CA8/Linux-amd64/bin/overmerry
CA8/Linux-amd64/bin/pbdagcon
CA8/Linux-amd64/bin/pbutgcns
CA8/Linux-amd64/bin/removeMateOverlap
CA8/Linux-amd64/bin/remove_fragment
CA8/Linux-amd64/bin/replaceUIDwithName-fastq
CA8/Linux-amd64/bin/replaceUIDwithName-posmap
CA8/Linux-amd64/bin/resolveSurrogates
CA8/Linux-amd64/bin/rewriteCache
CA8/Linux-amd64/bin/runCA
CA8/Linux-amd64/bin/runCA-dedupe
CA8/Linux-amd64/bin/runCA-overlapStoreBuild
CA8/Linux-amd64/bin/run_greedy.csh
CA8/Linux-amd64/bin/sffToCA
CA8/Linux-amd64/bin/show-corrects
CA8/Linux-amd64/bin/splitUnitigs
CA8/Linux-amd64/bin/terminator
CA8/Linux-amd64/bin/tigStore
CA8/Linux-amd64/bin/tracearchiveToCA
CA8/Linux-amd64/bin/tracedb-to-frg.pl
CA8/Linux-amd64/bin/trimFastqByQVWindow
CA8/Linux-amd64/bin/uidclient
CA8/Linux-amd64/bin/unitigger
CA8/Linux-amd64/bin/upgrade-v8-to-v9
CA8/Linux-amd64/bin/upgrade-v9-to-v10
CA8/Linux-amd64/bin/utg2fasta
CA8/Linux-amd64/bin/utgcns
CA8/Linux-amd64/bin/utgcnsfix
bin/MasurcaCelera.pm
bin/MasurcaCommon.pm
bin/MasurcaConf.pm
bin/MasurcaPaths.pm
bin/MasurcaSoap.pm
bin/MasurcaSuperReads.pm
bin/SOAPdenovo-127mer
bin/SOAPdenovo-63mer
bin/addSurrogatesToFrgCtgFile
bin/addSurrogatesToFrgctg.perl
bin/add_missing_mates.pl
bin/add_pb_seq.pl
bin/annotate
bin/blast_self_alignment_filter.pl
bin/bloom_query
bin/break_contigs.pl
bin/build_human_reference.sh
bin/chromosome_scaffolder.sh
bin/classify_reads.pl
bin/closeGaps.oneDirectory.fromMinKmerLen.perl
bin/closeGaps.oneDirectory.perl
bin/closeGaps.perl
bin/closeGapsInScaffFastaFile.perl
bin/closeGapsLocally.perl
bin/close_gaps.sh
bin/close_scaffold_gaps.sh
bin/collectReadSequencesForLocalGapClosing
bin/combineMUMs
bin/compute_contig_positions.pl
bin/compute_coverage.pl
bin/compute_sr_cov.pl
bin/compute_sr_cov.revisedForGCContig.pl
bin/correct_with_k_unitigs.sh
bin/correct_with_k_unitigs_fast.pl
bin/createFastaSuperReadSequences
bin/createKUnitigMaxOverlaps
bin/createSuperReadSequenceAndPlacementFileFromCombined.perl
bin/createSuperReadsForDirectory.perl
bin/create_end_pairs.perl
bin/create_end_pairs.pl
bin/create_k_unitigs_large_k
bin/create_k_unitigs_large_k2
bin/create_mega_reads
bin/create_merged_mega-reads.pl
bin/create_merged_sequences.pl
bin/create_sr_frg
bin/create_sr_frg.pl
bin/deduplicate_contigs.sh
bin/deduplicate_unitigs.sh
bin/delta-filter
bin/delta2vcf
bin/determineUnjoinablePacbioSubmegas.perl
bin/dnadiff
bin/eliminateBadSuperReadsUsingList
bin/error_corrected2frg
bin/evaluate_splits.pl
bin/exact-tandems
bin/expand_fastq
bin/extendSuperReadsBasedOnUniqueExtensions
bin/extendSuperReadsForUniqueKmerNeighbors
bin/extractJoinableAndNextPassReadsFromJoinKUnitigs.perl
bin/extract_merges.pl
bin/extract_merges_mega-reads.pl
bin/extract_unique_mega-reads.pl
bin/extract_unjoined_pairs.pl
bin/extractreads.pl
bin/extractreads_not.pl
bin/fasta2frg.pl
bin/fasta2frg_m.pl
bin/fasta_make_Nbase_bed.pl
bin/fastqToFasta.pl
bin/fill_unaligned_gaps.pl
bin/filter_alt.pl
bin/filter_delta_file_for_qrys.pl
bin/filter_library.sh
bin/filter_overlap_file
bin/filter_redundancy.pl
bin/finalFusion
bin/final_polish.sh
bin/findGapsInCoverageOfPacbios
bin/findMatchesBetweenKUnitigsAndReads
bin/find_contained_reads.pl
bin/find_repeats.pl
bin/fix_consensus_from_vcf.pl
bin/fix_unitigs.sh
bin/flye
bin/flye-assemble
bin/flye-contigger
bin/flye-minimap2
bin/flye-polish
bin/flye-repeat
bin/fragScaff.pl
bin/fragScaff.sh
bin/freebayes
bin/getATBiasInCoverageForIllumina_v2
bin/getEndSequencesOfContigs.perl
bin/getGCBiasStatistics.perl
bin/getLengthStatisticsForKUnitigsFile.perl
bin/getMeanAndStdevByGCCount.perl
bin/getMeanAndStdevForGapsByGapNumUsingCeleraAsmFile.perl
bin/getMeanAndStdevForGapsByGapNumUsingCeleraTerminatorDirectory.perl
bin/getNumBasesPerReadInFastaFile.perl
bin/getSequenceForClosedGaps.perl
bin/getSequenceForLocallyClosedGaps.perl
bin/getSuperReadInsertCountsFromReadPlacementFile
bin/getSuperReadInsertCountsFromReadPlacementFileTwoPasses
bin/getSuperReadPlacements.perl
bin/getUnitigTypeFromAsmFile.perl
bin/get_super_read_sizes
bin/get_super_read_sizes.pl
bin/homo_trim
bin/insert_repeats.pl
bin/introduce_errors_fasta_file.pl
bin/jellyfish
bin/jf_aligner
bin/joinKUnitigs_v3
bin/join_mega_reads_trim.onepass.nomatch.pl
bin/join_mega_reads_trim.onepass.pl
bin/join_mega_reads_trim.onepass.ref.pl
bin/join_mega_reads_trim.onepass.rna.pl
bin/killBadKUnitigs
bin/longest_path
bin/makeAdjustmentFactorsForNumReadsForAStatBasedOnGC
bin/makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2
bin/make_mate_frg.pl
bin/make_mr_frg.pl
bin/make_rejoin_links.pl
bin/masurca
bin/masurca-superreads
bin/mega_reads_assemble_cluster.sh
bin/mega_reads_assemble_cluster2.sh
bin/mega_reads_assemble_polish.sh
bin/mega_reads_assemble_ref.sh
bin/mergeSuperReadsUniquely.pl
bin/merge_contigs.pl
bin/merge_coords
bin/merge_matches_and_tile_coords_file.pl
bin/merge_matches_and_tile_coords_file_new.pl
bin/merge_mate_pairs
bin/merge_mega-reads.pl
bin/merge_sequences_simple.pl
bin/mummer
bin/mummerplot
bin/nucmer
bin/outputAlekseysJellyfishReductionFile.perl
bin/outputJoinedPairs.perl
bin/outputRecordsNotOnList
bin/output_reconciled_scaffolds.pl
bin/parallel_delta-filter.sh
bin/polca.sh
bin/polish_with_illumina_assembly.sh
bin/process_scaffold_gaps.pl
bin/promer
bin/quorum
bin/quorum_create_database
bin/quorum_error_correct_reads
bin/recompute_astat_superreads.sh
bin/recompute_astat_superreads_CA8.sh
bin/reconcile_consensus.pl
bin/reconcile_matches.pl
bin/reconciliate_mega_reads.maximal.nucmer.pl
bin/recover_scaffolds.pl
bin/reduce_sr
bin/refine.sh
bin/refine_alignments.pl
bin/rename_filter_fastq
bin/rename_filter_fastq.pl
bin/repeat-match
bin/resolve_trio.sh
bin/restore_ns.pl
bin/reverse_complement
bin/runByDirectory
bin/runSRCA.pl
bin/run_ECR.sh
bin/samToDelta
bin/samba.sh
bin/sample_mate_pairs.pl
bin/samtools
bin/show-aligns
bin/show-coords
bin/show-diff
bin/show-snps
bin/show-tiling
bin/sizesToScaff.pl
bin/sorted_merge
bin/splitFileAtNs
bin/splitFileByPrefix.pl
bin/splitLongKUnitigs.pl
bin/splitScaffoldsAtNs.pl
bin/splitScaffoldsAtNs.sh
bin/split_long_unitigs.pl
bin/split_matches_file.pl
bin/split_mate_pairs
bin/split_reads_to_join.pl
bin/translateReduceFile.perl
bin/translate_reduced_reads.pl
bin/trim_by_kunitigs.pl
bin/trim_mega_reads.pl
bin/ufasta
include/jellyfish-1/jellyfish/allocators_mmap.hpp
include/jellyfish-1/jellyfish/atomic_bits_array.hpp
include/jellyfish-1/jellyfish/atomic_field.hpp
include/jellyfish-1/jellyfish/atomic_gcc.hpp
include/jellyfish-1/jellyfish/backtrace.hpp
include/jellyfish-1/jellyfish/binary_dumper.hpp
include/jellyfish-1/jellyfish/bloom_common.hpp
include/jellyfish-1/jellyfish/bloom_counter2.hpp
include/jellyfish-1/jellyfish/bloom_filter.hpp
include/jellyfish-1/jellyfish/circular_buffer.hpp
include/jellyfish-1/jellyfish/compare_and_swap.hpp
include/jellyfish-1/jellyfish/cooperative_pool.hpp
include/jellyfish-1/jellyfish/cooperative_pool2.hpp
include/jellyfish-1/jellyfish/cpp_array.hpp
include/jellyfish-1/jellyfish/divisor.hpp
include/jellyfish-1/jellyfish/dumper.hpp
include/jellyfish-1/jellyfish/err.hpp
include/jellyfish-1/jellyfish/file_header.hpp
include/jellyfish-1/jellyfish/generator_manager.hpp
include/jellyfish-1/jellyfish/generic_file_header.hpp
include/jellyfish-1/jellyfish/hash_counter.hpp
include/jellyfish-1/jellyfish/int128.hpp
include/jellyfish-1/jellyfish/jellyfish.hpp
include/jellyfish-1/jellyfish/json.h
include/jellyfish-1/jellyfish/large_hash_array.hpp
include/jellyfish-1/jellyfish/large_hash_iterator.hpp
include/jellyfish-1/jellyfish/locks_pthread.hpp
include/jellyfish-1/jellyfish/mapped_file.hpp
include/jellyfish-1/jellyfish/mer_dna.hpp
include/jellyfish-1/jellyfish/mer_dna_bloom_counter.hpp
include/jellyfish-1/jellyfish/mer_heap.hpp
include/jellyfish-1/jellyfish/mer_iterator.hpp
include/jellyfish-1/jellyfish/mer_overlap_sequence_parser.hpp
include/jellyfish-1/jellyfish/mer_qual_iterator.hpp
include/jellyfish-1/jellyfish/misc.hpp
include/jellyfish-1/jellyfish/offsets_key_value.hpp
include/jellyfish-1/jellyfish/parser_common.hpp
include/jellyfish-1/jellyfish/rectangular_binary_matrix.hpp
include/jellyfish-1/jellyfish/sam_format.hpp
include/jellyfish-1/jellyfish/simple_circular_buffer.hpp
include/jellyfish-1/jellyfish/sorted_dumper.hpp
include/jellyfish-1/jellyfish/stdio_filebuf.hpp
include/jellyfish-1/jellyfish/storage.hpp
include/jellyfish-1/jellyfish/stream_iterator.hpp
include/jellyfish-1/jellyfish/stream_manager.hpp
include/jellyfish-1/jellyfish/text_dumper.hpp
include/jellyfish-1/jellyfish/thread_exec.hpp
include/jellyfish-1/jellyfish/time.hpp
include/jellyfish-1/jellyfish/token_ring.hpp
include/jellyfish-1/jellyfish/whole_sequence_parser.hpp
include/mummer-1/include/compactsufsort/compactsufsort.hpp
include/mummer-1/include/compactsufsort/compactsufsort_imp.hpp
include/mummer-1/include/compactsufsort/const_iterator_traits.hpp
include/mummer-1/include/compactsufsort/divsufsort_private.h
include/mummer-1/include/compactsufsort/said_traits.hpp
include/mummer-1/include/compactsufsort/sssort_imp.hpp
include/mummer-1/include/compactsufsort/trsort_imp.hpp
include/mummer-1/include/jellyfish/circular_buffer.hpp
include/mummer-1/include/jellyfish/cooperative_pool2.hpp
include/mummer-1/include/jellyfish/cpp_array.hpp
include/mummer-1/include/jellyfish/divisor.hpp
include/mummer-1/include/jellyfish/stream_manager.hpp
include/mummer-1/include/jellyfish/whole_sequence_parser.hpp
include/mummer-1/include/mt_skip_list/common.hpp
include/mummer-1/include/mt_skip_list/set.hpp
include/mummer-1/include/mummer/48bit_index.hpp
include/mummer-1/include/mummer/48bit_iterator.hpp
include/mummer-1/include/mummer/const_iterator_traits.hpp
include/mummer-1/include/mummer/delta.hh
include/mummer-1/include/mummer/dset.hpp
include/mummer-1/include/mummer/fasta.hpp
include/mummer-1/include/mummer/mgaps.hh
include/mummer-1/include/mummer/nucmer.hpp
include/mummer-1/include/mummer/openmp_qsort.hpp
include/mummer-1/include/mummer/postnuc.hh
include/mummer-1/include/mummer/redirect_to_pager.hpp
include/mummer-1/include/mummer/sparseSA.hpp
include/mummer-1/include/mummer/sparseSA_imp.hpp
include/mummer-1/include/mummer/sw_align.hh
include/mummer-1/include/mummer/sw_alignscore.hh
include/mummer-1/include/mummer/tigrinc.hh
include/mummer-1/include/mummer/timer.hpp
include/mummer-1/include/mummer/translate.hh
include/mummer-1/include/thread_pipe.hpp
include/mummer-1/include/thread_pipe/circular_buffer.hpp
include/mummer-1/include/thread_pipe/cooperative_pool2.hpp
include/mummer-1/include/thread_pipe/divisor.hpp
include/mummer-1/include/thread_pipe/traits.hpp
include/samtools/bam.h
include/samtools/bam2bcf.h
include/samtools/bam_endian.h
include/samtools/bam_tview.h
include/samtools/bcftools/bcf.h
include/samtools/bcftools/kmin.h
include/samtools/bcftools/prob1.h
include/samtools/bgzf.h
include/samtools/errmod.h
include/samtools/faidx.h
include/samtools/kaln.h
include/samtools/khash.h
include/samtools/klist.h
include/samtools/knetfile.h
include/samtools/kprobaln.h
include/samtools/kseq.h
include/samtools/ksort.h
include/samtools/kstring.h
include/samtools/razf.h
include/samtools/sam.h
include/samtools/sam_header.h
include/samtools/sample.h
lib/global/Foundation.pm
lib/global/tandem-repeat.awk
lib/libbam.a
lib/libbam.so
lib/libbam.so.0
lib/libbam.so.0.0.0
lib/libbcf.a
lib/libbcf.so
lib/libbcf.so.0
lib/libbcf.so.0.0.0
lib/libjellyfish-2.0.a
lib/libjellyfish-2.0.so
lib/libjellyfish-2.0.so.2
lib/libjellyfish-2.0.so.2.0.0
lib/libumdmummer.a
lib/libumdmummer.so
lib/libumdmummer.so.0
lib/libumdmummer.so.0.0.0
lib/perl/jellyfish.a
lib/perl/jellyfish.pm
lib/perl/jellyfish.so
lib/perl/jellyfish.so.0
lib/perl/jellyfish.so.0.0.0
lib/perl/mummer.a
lib/perl/mummer.pm
lib/perl/mummer.so
lib/perl/mummer.so.0
lib/perl/mummer.so.0.0.0
lib/pkgconfig/jellyfish-2.0.pc
lib/pkgconfig/mummer.pc
libexec/global/mgaps
libexec/global/postnuc
libexec/global/postpro
libexec/global/prepro
share/adapter.jf
share/man/man1/jellyfish.1
