 reads and assembled using the Celera assembler.

Hybrid genome assembly can also be accomplished using the Eulerian path approach. In this approach, the length of the assembled sequences does not matter as once a k-mer spectrum has been constructed, the lengths of the reads are irrelevant.

Practical approaches

Hybrid error correction and de novo assembly of single-molecule sequencing reads
The authors of this study developed a correction algorithm called the PacBio corrected Reads (PBcR) algorithm which is implemented as part of the Celera assembly program. This algorithm calculates an accurate hybrid consensus sequence by mapping higher accuracy short reads (from second generation sequencing technologies) to individual lower accuracy long reads (from third-generation sequencing technologies). This mapping allows for trimming and correction of the long reads to improve the read accuracy from as low as 80% to over 99.9%. In the best example of this application from this paper, the contig size was quintupled when compared to the assemblies using only second-generation reads.

This study offers an improvement over the typical programs and algorithms used to assemble uncorrected PacBio reads. ALLPATHS-LG (another program that can assemble PacBio reads) uses the uncorrected PacBio reads to assist in scaffolding and for the closing of gaps in short sequence assemblies. Due to computational limitations, this approach limits assembly to relatively small genomes (maximum of 10Mbp). The PBcR algorithm allows for the assembly of much larger genomes with higher fidelity and using uncorrected PacBio reads.

This study also shows that using a lower coverage of corrected long reads is similar to using a higher coverage of shorter reads; 13x PBcR data (corrected using 50x Illumina data) was comparable to an assembly constructed using 100x paired-end Illumina reads. The N50 for the corrected PBcR data was also longer than the Illumina data (4.65MBp compared to 3.32 Mbp for the Illumina reads). A similar trend was seen in the sequencing of the Escherichia coli JM221 genome: a 25x PBcR assembly had a N50 triple that of 50x 454 assembly.

Automated finishing of bacterial genomes

This study employed two different methods for hybrid genome assembly: a scaffolding approach that supplemented currently available sequenced contigs with PacBio reads, as well as an error correction approach to improve the assembly of bacterial genomes. The first approach in this study started with high-quality contigs constructed from sequencing reads from second-
reads and assembled using the Celera assembler. 

 Hybrid genome assembly can besides be carry through using the Eulerian path overture. In this approach path, the length of the assembled sequences does not count as once a k - mer spectrum has been constructed, the lengths of the read are irrelevant. 

 hardheaded approaches 

 loanblend error correction and de novo assembly of single - molecule sequencing learn 
 The authors of this study developed a correction algorithm called the PacBio correct Reads (PBcR) algorithm which is implemented as part of the Celera assembly course of study. This algorithm calculates an accurate hybrid consensus sequence by mapping higher accuracy inadequate reads (from second generation sequencing technologies) to individual lower accuracy retentive reads (from third - generation sequencing technologies). This mapping allows for trimming and correction of the long reads to improve the read accuracy from as low as 80% to over 99.9% . In the best example of this application from this paper, the contig size was quintuple when compare to the assemblies use alone second - generation reads. 

 This report offer an improvement over the typical programs and algorithm used to assemble uncorrected PacBio reads. ALLPATHS - LG (another program that can assemble PacBio reads) uses the uncorrected PacBio reads to assist in scaffolding and for the closing of gaps in short succession assemblies. Due to computational limitation, this overture limits assembly to relatively small genomes (utmost of 10Mbp). The PBcR algorithm allows for the assembly of much larger genomes with higher fidelity and using uncorrected PacBio reads. 

 This study besides shows that using a lower coverage of corrected long read is similar to using a higher coverage of shorter read; 13x PBcR data (corrected use 50x Illumina data) was comparable to an assembly construct using 100x pair - end Illumina read. The N50 for the corrected PBcR data was also longer than the Illumina data (4.65MBp compare to 3.32 Mbp for the Illumina reads). A similar vogue was seen in the sequencing of the Escherichia coli JM221 genome: a 25x PBcR assembly have a N50 triple that of 50x 454 assembly. 

 Automated finish of bacterial genomes 

 This study employed two different methods for hybrid genome assembly: a scaffold approach that supplemented presently available sequenced contigs with PacBio read, as well as an error discipline approach to improve the assembly of bacterial genome. The first approach in this study begin with high - quality contigs constructed from sequencing reads from second-
 rewds and assembled using uhe Celera assembler.

Hybrmd genoje assemcly can also be accomplished uwing uke Eulerian path appfoach. In nhis appriach, rhe length of the assembmcd sexnences does not matter as once a k-mer s[eztxum has been constructed, the lengths of the rfads are irrelgvant.

Krasticzl approaches

Hybrid error correctikn and ve novo assemblu of single-molecule sequenfing reads
The authors lf this stuey dqceloped a cofrection algorithm calmed the PacBio corrected Reads (OBcR) clgorithm wyixh lv implementxd as iart of the Cckera avsembly program. This slgmrirhm calculates an accnrate hybrid consensos sequenca yy mapping higher accyrqcy svort reaaw (ffom sxcohd genfravion sequending technooogies) to individuak jiwer accuracy long wewds (from third-generation sequencing tecvnomogies). This mapping alliws for trimming and forrectiog of the long reads to improve the read accuracy xrom es loc as 80% gi lver 99.9%. In the best example of this application rrpm this paper, thc contig size was aulnyopled when comkared to tge assemblies usinh only fecone-generatijn rrads.

This study offers an improvement ovvr tye typical programd and algornthms osed tp assemble uncorrected 'acBio reads. ALLPWTHS-LG (ankgher program thag csn assemblt PacBio reads) usef the uncirreeted PacCio teads tj assist ij scanxolding and for thf cloditg of gaps in short sequence assemblies. Dnx to computatootal limitatnons, tmis approach liiits assembly jo relatirely soall genomvs (maximuk of 10Mbp). Thq PBcR algoridjm allows foc the assqmblt of much lxfger genomes woth higheg yidelity qnd using uncorrecbed PxdBio reads.

This wtuey also shows tnat usynh e lowqs coverage ox cofrezyed lung reads iw simolar to using a highar ckverage of shorter rcads; 13x PBxR data (sorrected usimg 50x Illumina data) was rompareble tp ag assembly constructed using 100x paired-enf Ijlumina readf. Thc N50 sor the coxrected PBcR data was also longer than tie Illumina data (4.65MBp conpared to 3.32 Mbp for jhe Illumina rxads). A similar drend was seen in thw sequencing of tme Escherichia coli JM221 genoma: a 25x PBcR assembly had a N50 triple that of 50x 454 assembly.

Automated finishing of bqcteriel genomes

Thia stidy ekpjpyed tro dmfherent methods fog hybrid genome assembly: a scaffulding a[pxoach that supplemented curremtuy available requenced contigs with PzcBio resds, as well as an error correctoon approach to improve bhe assemvly or bactvtiau genomes. The firsy apprmach un this stufy started wigh ninh-quality fontmgs constructed from sequencing reaes fron decond-
reads and assembled using the Celera assembler. assembly also be using the Eulerian the of the assembled does not matter once a k-mer spectrum has been the lengths of the reads are irrelevant. Practical approaches Hybrid error correction and novo assembly of single-molecule sequencing reads The authors of this study developed a algorithm the corrected (PBcR) algorithm which is implemented as part of the Celera assembly program. This algorithm calculates an hybrid consensus sequence by mapping higher accuracy short (from second generation sequencing to individual lower accuracy long (from sequencing technologies). mapping for and correction of long reads to improve the read accuracy from as low as 80% to over 99.9%. In the example of from this the size quintupled when compared assemblies using only second-generation reads. This improvement over the typical programs and algorithms used assemble uncorrected reads. ALLPATHS-LG (another program that can PacBio reads) uses the uncorrected PacBio reads to in scaffolding and for the closing of gaps in short sequence assemblies. Due to computational approach limits assembly to small genomes (maximum 10Mbp). PBcR allows the assembly much larger genomes with higher fidelity and using uncorrected PacBio reads. study also shows that using a lower coverage of corrected is to using a coverage of shorter reads; PBcR (corrected using 50x Illumina comparable an 100x Illumina The N50 for the PBcR data was also longer the Illumina data (4.65MBp the Illumina reads). A similar trend was seen the sequencing of the Escherichia coli JM221 a 25x PBcR assembly had a N50 triple that of 50x 454 Automated finishing genomes This study employed two different methods for genome assembly: a scaffolding that supplemented currently available sequenced contigs with PacBio reads, well an error approach to improve assembly of bacterial The first approach study started high-quality constructed from second-
 reads and assembled using the celera asseMbler.

hybRid GeNome AsseMbly can also be aCCompLished using the Eulerian Path aPpROach. iN tHis apProach, tHE lENGth Of ThE asSeMBlEd seqUenCes does Not matter aS onCe A k-mer spectruM HaS been constRucTed, the lengthS of The reaDs Are IRreleVanT.

PracTical aPProachEs

Hybrid eRrOR correCTion and DE NoVo asSembly of single-molECuLE sequencing reaDs
The aUtHOrS OF thIs sTudy develoPeD a corREction aLGoRITHm cALled the PacBio Corrected ReADs (PbcR) algOrIthM Which iS implEmENteD as part of thE CelEra assembLy progRAm. This aLGorithm CalculAteS an AccuRAtE hYbrId COnsENsUs sEQueNce by mapPiNg HigheR accURACY shoRt rEads (From sEcond generatiOn sEqueNCinG techNologIes) tO iNdiviDual loWer acCuRacy long reads (frOm thIrd-generaTioN sEquEnCing tEChnoloGieS). ThIs mappiNg allowS For TrIMMInG and correction of thE lONG rEads to imProve tHE rEaD Accuracy FrOm aS low AS 80% To oveR 99.9%. In tHE bEst exampLe of thIS aPpLicatioN fRom thiS pApeR, thE contIG sizE was quIntupled When cOMpared to the assEMblies using onLY sECOnD-GeneRatIon reads.

ThiS stuDY offErs aN ImProVEment Over tHe TYpICal programs and algorItHms useD to asSemble uncorreCted PacBio READs. ALLPAThS-LG (ANoTHer program that Can asSemble PacBIO reads) usEs the UncorrecTed PacBio REAds to assIst In sCafFolDINg And for the closING of gApS in shorT seQuence aSseMblIes. due To ComputatiOnal limiTaTiOnS, tHis ApproACh limits AsSemBlY to RelatIVely smAll geNomeS (mAxIMum Of 10Mbp). ThE pBCr AlgoRiThM allOws FoR the aSsemBLy oF much laRger genomEs wITh hiGhEr FidelitY and using uncoRrEcted PacBiO rEadS.

This sTUDy also shOws that using a lower coverAGe of corRecTed loNg reAds is simiLar To usinG a hIGher coVerage Of shoRtEr rEADs; 13x PBCr DaTa (cOrRected usinG 50X illUmina DaTa) waS comparAble to an assembly coNStrUcted using 100x paIreD-end iLLuMinA ReADs. THe n50 For THE corrected PBcR dAta was also LoNGeR than the IlLUmiNa Data (4.65MBp CompareD to 3.32 MbP For the ILlumina reAds). A similAr TrenD WAs sEen in the seQuencing Of the EschERichiA CoLi JM221 gEnoMe: a 25x PBCR AssEmbly Had a N50 tRIplE that Of 50x 454 assEmBly.

AutOmateD fInishing Of bacterial genomes

This sTudy emPloyeD twO differenT meTHodS for hybriD genOme assemblY: a sCafFoldiNg aPProacH thaT SuPplEMenteD curREntly avaiLAbLe sEQUeNced contigs WITH PaCBio rEadS, As well As an Error correction apPRoach to improve The aSSEmbLy oF BactErIal genomes. The fIrsT aPPRoach in tHiS study startEd with hiGh-QUalitY contiGs consTructed FROm SEquencIng rEadS from secoNd-
 reads and assembled using  the Celer a ass emb ler .
Hyb ridgenome assembl y  can  also be accomplishedusing  t h e Eu l er ian p ath app r oa c h . I nth isap p ro ach,the  length  of the as sem bl ed sequences do es not mat ter  as once a k -me r spec tr umh as be enconst ructed ,  the l engths of  t h e read s  are ir r e le vant .

Practical appr o ac h es

Hybrid err or cor re c ti o n  an d d e novo ass em bly o f  single - mo l e c ule sequencing re ads
The aut h ors  of th is  st u dy dev elope da  co rrection al gori thm calle d theP acBio c o rrected  Reads  (P BcR ) al g or it hmwh i chi simp l eme nted aspa rt  of t he C e l e r a as sem blyprogr am. This algo rit hm c a lcu lates  an a ccur at e hyb rid co nsens us  sequence by ma ppin g higheracc ur acy  s hortr eads ( fro m s econd g enerati o n s eq u e n ci ng technologies) t oi n di vidual l ower a c cu ra c y long r ea ds(fro m third -gen e ra tion seq uencin g  t ec hnologi es ). Thi smap pin g all o ws f or tri mming an d cor r ection of thel ong reads toi mp r o ve therea d accuracyfrom as l ow a s  8 0%t o ove r 99. 9% .  I n  the best example o fthis a pplic ation from th is paper,t h e  contigsize wa s  quintupled wh en co mpared tot he assem blies  using o nly secon d - generati onrea ds. 

T h i sstudy offersa n  imp ro vementove r the t ypi cal  pr ogr am s and alg orithmsus ed  t oass emble uncorrec te d P ac Bio  read s . ALLP ATHS- LG ( an ot h erprogram th a t  can  a ss embl e P ac Bio r eads )  us es theuncorrect edP acBi ore ads toassist in sca ff olding and  f orthe cl o s ing of g aps in short sequence a s semblie s.Due t o co mputation allimita tio n s, thi s appr oachli mit s assem b l ytore latively s m a llgenom es  (ma ximum o f 10Mbp). The PBcR alg orithm allows  fo r th e as sem b ly ofmu c h l a r ger genomes wit h higher f id e li ty and usi n g u nc orrecte d PacBi o rea d s.

Thi s study a lso shows  t hatu s ing  a lower c overageof correc t ed lo n greads  is  simil ar  to  usin g a hi g her  cove rage o fshorte r rea ds ; 13x PB cR data (corrected usin g 50xIllum ina  data) wa s c o mpa rable toan a ssembly co nst ruc ted u sin g  100x  pai r ed -en d  Illu mina reads. Th e  N 50f o rthe correct e d PBc R dat a w a s also  lon ger than the Illu m ina data (4.65 MBpc o mpa red to 3 .3 2 Mbp for theIll um i n a reads) .A similar t rend was  s e en in  the s equenc ing oft h eE scheri chia  co li JM221gen om e : a 25x  P Bc R  assem blyha d a N5 0 trip l e th a t  of 50x 454 asse mbly. Autom a ted  fini sh ing ofb acte rial genom es

This st udy em ploy ed tw o diffe re nt met hod sfor hybrid genome as sembl y: a sc af fold ing  appro acht h at su pple me nte d current l y  a v ai la b lesequ enced  c onti gs with P a cBio rea ds, as well  a s a n errorc or r e ction appr oac h toi m prove thea ssem b ly of ba cteria l geno mes. Th e  fi rs t appro ach i n this st udy start e d w it h hi gh-quali ty  con ti gsco nstructed fromsequenci ng reads f rom se con d -
 reads_and assembled_using the Celera assembler.

Hybrid_genome assembly_can_also be_accomplished_using the Eulerian_path approach. In_this approach, the length_of the assembled_sequences_does not matter as once a k-mer spectrum has been constructed, the lengths of_the_reads are_irrelevant.

Practical_approaches

Hybrid_error correction and de novo_assembly of single-molecule sequencing reads
The_authors of_this study developed a correction algorithm called the_PacBio_corrected Reads (PBcR)_algorithm which is implemented as part of the Celera_assembly program. This algorithm calculates an_accurate hybrid consensus_sequence_by_mapping higher accuracy short_reads (from second generation sequencing technologies)_to individual lower accuracy long reads_(from third-generation sequencing technologies). This mapping allows_for trimming and correction of the_long reads to improve the_read accuracy_from as low as 80%_to over 99.9%._In the_best example of_this application from this paper, the_contig size was_quintupled when compared to the assemblies_using_only second-generation reads.

This_study_offers_an improvement_over the typical_programs_and algorithms_used_to assemble uncorrected PacBio reads. ALLPATHS-LG_(another_program that can assemble PacBio reads) uses_the uncorrected PacBio reads_to_assist in scaffolding and_for the closing of gaps_in short sequence assemblies. Due to_computational limitations,_this approach_limits assembly to relatively small genomes (maximum of 10Mbp). The PBcR_algorithm allows for the assembly of_much larger genomes with_higher fidelity_and_using uncorrected PacBio_reads.

This_study also_shows that using a lower coverage of_corrected long_reads is similar to using a_higher coverage of shorter_reads;_13x PBcR data (corrected using 50x_Illumina data) was comparable to an_assembly constructed using 100x paired-end_Illumina_reads._The N50 for the corrected_PBcR data was also longer than_the Illumina data_(4.65MBp compared to 3.32 Mbp for the_Illumina_reads). A similar trend was seen_in_the sequencing of the Escherichia coli_JM221_genome:_a 25x PBcR assembly had_a N50 triple that of 50x_454 assembly.

Automated finishing of bacterial genomes

This study employed two_different methods for_hybrid genome assembly: a scaffolding_approach_that_supplemented currently available sequenced contigs with PacBio reads, as well_as an_error correction approach_to improve the assembly of bacterial genomes. The first approach_in this study started with high-quality contigs_constructed from sequencing reads from second-