CISA statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool CISA

Tool usage distribution map

This map represents all the scientific publications referring to CISA per scientific context
info info

Associated diseases

This word cloud represents CISA usage per disease context

Popular tool citations

chevron_left Assembly reconciliation chevron_right
Want to access the full stats & trends on this tool?


CISA specifications


Unique identifier OMICS_09320
Alternative name Contig Integrator for Sequence Assembly
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data MUMmer, BLAST+
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Yu-Chieh Liao

Publication for Contig Integrator for Sequence Assembly

CISA citations


Genome Sequence of Coxiella Like Endosymbiont Strain CLE RmD, a Bacterial Agent in the Cattle Tick, Rhipicephalus microplus Deutsch Strain

Genome Announc
PMCID: 5876479
PMID: 29599150
DOI: 10.1128/genomeA.00003-18
call_split See protocol

[…] tracted using SAMtools v1.3.1 () and independently assembled into scaffolds using the state-of-the-art assemblers SPAdes v3.10.1 (), Velvet v1.2.10 (), and CLC Genomics Workbench v9.5.2 (Qiagen). The CISA v1.3 tool () was used to integrate the three de novo assemblies with the NCBI R. microplus CLE contigs into a hybrid set of scaffolds, from which duplicate regions were excluded.The partial genom […]


Whole genome sequencing of Leptospira interrogans from southern Brazil: genetic features of a highly virulent strain

PMCID: 5722262
PMID: 29236923
DOI: 10.1590/0074-02760170130

[…] Technologies). Genome assembly and annotation - De novo genome assembly was generated by MIRA (, Newbler (, and SPAdes (), and their results were merged by CISA () to generate a consensus assembly. The scaffolds of each chromosome were separated using BLAST searches against the genome of L. interrogans strain Fiocruz L1-130 (GenBank: AE016823.1, AE016824 […]


Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates

BMC Genomics
PMCID: 5748942
PMID: 29291727
DOI: 10.1186/s12864-017-4249-6

[…] tory assembly using SPAdes (v3.6.1) [], using the previous Velvet assembly as known data and changing the set of trial k-mers in each. All three resulting assemblies were integrated with the software CISA (v1.3) []. […]


Complete genome sequence of native Bacillus cereus strains isolated from intestinal tract of the crab Ucides sp.

PMCID: 5723261
PMID: 29234696
DOI: 10.1016/j.dib.2017.11.049
call_split See protocol

[…] ssemblies were generated for each strain using MIRA (, SPAdes and Newbler (, and for each strain a consensus assembly was generated using CISA . The final set of contigs from each strain was ordered with the program CAR , which is able to identify genome inversions and transpositions, using the genome of Bacillus cereus strain 03BB102 ( […]


Draft Genome Sequence of Klebsiella pneumoniae OK8, a Multidrug Resistant Mouse and Human Pathogen

Genome Announc
PMCID: 5597776
PMID: 28912335
DOI: 10.1128/genomeA.01018-17

[…] reads were assembled into genomic contigs using tools, namely, the A5 pipeline (), Edena (), MaSuRCA (), and SPAdes (). We found 5 contigs for the bacterial sample, and all contigs were merged using CISA (). Sequence annotation was carried out with the contigs using the Glimmer-MG program (). The predicted open reading frames (ORFs) were annotated using our in-house pipeline, CANoPI (Contig Annot […]


Draft Genome Sequence of Deinococcus indicus DR1, a Novel Strain Isolated from a Freshwater Wetland

Genome Announc
PMCID: 5543649
PMID: 28774987
DOI: 10.1128/genomeA.00754-17

[…] d to discard duplicates (). This filtration resulted in 40 contigs, with a GC content of 69% and sizes ranging from 989,508 to 10,905 bp (mean length, 111,690.7 bp), containing 4,467,628 bp in total. CISA was used to perform the final de novo assembly of contigs (). Annotation of the assembled genome was performed by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP).The draft genome contains […]

Want to access the full list of citations?
CISA institution(s)
Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan

CISA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review CISA