combination of alignment to reference genome SNP calling and velvet of unmapped contigs v. 2014-11
Canu v. v1.5; Racon v. v3.4.3; Circlator v. v1.5.5; Pilon v. v1.22
flye v2.5; minimap v0.2-r124; racon v1.1.0; circlator v1.5.3; Pilon v1.18; SPAdes v3.11.1; A5-miseq v20140604
SMRT v. 8.0.0, HGAP v. 4, SPAdes v. 3.11.1
PacBio Hierarchical Genome Assembly Process v. 3
RS_HGAP_Assembly.3 protocol v. 2.2.0; BWA v. 07.7.17; Unicycler v. 0.4.8
HGAP v.3 as available in the SMRT Analysis v. 2.3; Geneious Reference Assembly v. 11.1
SPAdes v. 3.1.1; CLC Genomics Workbench Tool v. 8.5.1
trycycler v. 0.5.3; unicycler v. 0.5.0; skesa v. 2.4.0
Flye v. v2.9; Minimap2 v. v2.24-r1122; Miniasm v. v0.3-r179; Racon v. v1.4.3; SPAdes v. v3.15
SMRT Link Microbial Assembly pipeline; output polished by Pilon v. 8.0
SMRT v. 8.0.0, HGAP v. 4, SPAdes v. 3.14.1
Celera Assembler v. Celera Assembler version 8.3
Canu v. 1.6; GapBlaster v. 1.1.2; MapSolver v. 3.2.0; Unicylcer v. 0.4.1; Circlator v. 1.5.2; Pilon v. 1.22
A5-miseq v. AUGUST-2016; MeDuSa v. 1.6; GapFiller v. 1.10
Newbler v. 2.6; Velvet v. 1.2.08; Allpaths v. 39750; Phrap v. SPS - 4.24
Flye v. 2.9; Medaka v. 1.6.1; Polca (Masurca) v. 4.0.5
SMRT v. 2.3.0; DNASTAR SeqMn NGen v. 11.0
MIRA v. 3.9.9; ABySS v. 1.3.4; PBJelly v. 12.9.14; CLC-bio v. 6.0.4; PAGIT v. 1; Celera v. 7.0
HGAP (part of Pacific Biosciences, SMRT Analysis Software) v. 3
HGAP v. 3; Geneious Reference Assembly v. 11.1
Hifiasm v. 0.13-r308; Canu v. 1.7; Pilon v. 1.22
SMRT v. 6.0.0, HGAP v. 4, SPAdes v. 3.11.1
Unicycler v. 0.4.4; Canu v. 1.8; Pilon v. 1.23
SOAPdenovo v. v2.04; Celera Assembler v. 8.0
HGAP v. May-2015; Celera Assembler v. May-2015; Quiver v. May-2015
Flye/Smrtlink v. 2.6 (Flye) / 8.0 (Smrtlink)
Unicycler hybrid assembly v. v0.4.8-beta
Unicycler (normal mode) using PE Illumina reads and filtered (>10k) ONT reads (Filtlong v0.2.0); contigs >2k v. v0.4.8
CLCbio CLC Genomics Workbench v. 7.5; PacBio SMRT Analysis v. 2.3.0
Celera Assembler v. May-2015; HGAP v. May-2015; Quiver v. May-2015
HGAP v. 2.3; Geneious Reference Assembly v. 11.1
Newbler v. v2.3; Geneious v. v5.1; Velvet v. v1.0.13
HGAP Assembly v. 3.0; Celera Assembler v. 8.2
SPAdes v. MAY-2020; unicycler v. MAY-2020
SMRT v. 7.1.0, HGAP v. 4, SPAdes v. 3.11.1
flye v. v2.8.3-b1695; medaka v. v1.5.0; Polypolish v. v0.5.0; POLCA v. v4.0.5
canu v. Canu snapshot v1.7 +242 changes (r8934)
Flye v. 2.9; Medaka v. 1.6.1; Polca (part of Masurca) v. 4.0.5
miniasm v. 0.2-r168-dirty; racon correction (3 iterations) v. 1.3.1; racon correction with Illumina reads v. 1.3.1
CLC Genomics Workbench v. 7.5.1; BacBio SMRT Analysis v. 2.3.0
Newbler v. 2.7; Velvet v. 1.1; ELANDv2e v. 1.8.2
CLC Genomics Workbench v. 9.5; Geneious v. R9; SPAdes v. 3.0.5
Newbler v. v2.3; Velvet v. v1.0.13; Geneious v. v5.1
Canu v. 1.3; GapFiller v. 1.11; PrlnSeS-G v. 1.0.0
SMRTAnalysis v. 2.2.0 pl build 134282; HGAP
CLCbio CLC Genomics Workbench v. 7.5.1; PacBio SMRT Analysis v. 2.3.0
Trycycler v. 0.5.3; Flye v. 2.9; Raven v. 1.8.0; Miniasm v. 0.3
RS_HGAP_Assembly.3 protocol v. 2.2.0; BWA v. 07.7.17
Unicycler v. 0.4.8.0; metaSPAdes v. 3.9.0; MaxBin2 v. 2.2.7+galaxy2
Ratatosk long read correction, followed byUnicycler v. 0.4.8
CLC Genomics Workbench v. 7.0; Celera Assembler v. 7.0
HGAP3.3 SMRT Pipeline v. 2.3.0; Pilon v. 1.21
Microbial Genome Analysis v. SMRT Link 11.0.0.146107
RS_HGAP.3 v. JULY-2016; Pilon v. NOVEMBER-2016
UniCycler v. 0.4.8; SPAdes v. 3.13.0; racon v. 1.4.3; NCBI Blast v. 2.9.0+; bowtie2 v. 2.3.5; samtools v. 1.9; java v. 1.8.0_181; pilon v. 1.23
PacBio smrtanalysis HGAP_3 algorithm v. NOV-2016
CLC v. 6.0; Edena v. 3.13; CISA v. 1.3; RAGOUt v. 2.0
Trycycler v. 0.4.1; Flye v. 2.8.3-b1695; Raven v. 1.5.0; Miniasm v. 0.3-r179; Minipolish v. 0.1.2
Canu v. 1.4; Pilon v. 1.22; MapSolver v. 3.2.0
DNASTAR SeqMan NGen v. 11.0.0; Lasergene
HGAP3 v. SMRTPortal v2.3.0; bwa v. 0.7.13; Pilon v. 1.22
HGAP_3 in SMRT analysis v. 2.3, Spades v. 3.5.0
Microbial Assembly v. SMRTanalysis v8.0; SKESA v. v 2.3.0
Trycycler v. 0.4.1; Flye v. 2.8.1; Raven v. 1.3.0; Canu v. 2.1.1; Miniasm/minipolish v. 0.3/0.1.2; Pilon v. 1.23; Medaka v. 1.2.1
SMRT v. 2.3.0, HGAP v. 3, SPAdes v. 3.6.0
HGAP Assembly v. 4.0; circlator v. 1.5.3; Pilon v. 1.18
HGAP Assembly v. 3.0; Pilon v. 1.18; A5 MiSeq v. 20140513
CANU v. v2.1.1; pepper v. v0.1.5; Homopolish v. v0.2.1
SMRT Analysis System v. smrtanalysis_2.3.0.140936.p2.144839; hgap3