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CISA specifications

Information


Unique identifier OMICS_09320
Name CISA
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

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Maintainer


  • person_outline Yu-Chieh Liao <>

Publication for Contig Integrator for Sequence Assembly

CISA in pipelines

 (5)
2017
PMCID: 5543649
PMID: 28774987
DOI: 10.1128/genomeA.00754-17

[…] 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 […]

2016
PMCID: 4749706
PMID: 26904016
DOI: 10.3389/fmicb.2016.00143

[…] if they matched at >95% nucleotide identity over more than 200 bp (figure , step 3). these contigs are putatively from the same organism or population as the sag contigs (). next, we used cisa () to combine the extracted metagenomic and the sag contigs into an integrated assembly (figure , step 4). for each newly generated contig, cisa reports which assembly provided the backbone. […]

2016
PMCID: 4778666
PMID: 26981415
DOI: 10.1016/j.gdata.2016.01.010

[…] 000 pb and with coverage larger than 10 × were selected resulting in 53 scaffolds. mira contigs smaller than 1000 pb were discarded, 91 contigs remained. with these two sets of scaffolds and contigs, cisa integrator v1.0.1 was used and a final set of 40 sequences was obtained. tools used for filtering and trimming and assembly programs are also included in galaxy orione web server. the 40 contigs […]

2016
PMCID: 4832037
PMID: 27114904
DOI: 10.1016/j.gdata.2016.02.013

[…] (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the bases with quality value bellow phred 20 were removed., draft genome was assembled using the packages velvet , mira and spades . cisa and lasergene v11 suite (dnastar) software were used to reduce the number of contigs. subsequently, the mauve software was applied to order the draft genome by using the genomes […]

2015
PMCID: 4536688
PMID: 26272577
DOI: 10.1128/genomeA.00910-15

[…] the whole-genome shotgun sequencing was performed using the illumina miseq platform with a paired-end library at macrogen. all three genomes were de novo assembled using a5 (), sga (), ray (), and cisa (). for the genome annotation, open reading frames (orfs) found by prodigal () were aligned against a data set of proteins from the leptospira genus from uniprot (http://www.uniprot.org) using […]


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CISA in publications

 (60)
PMCID: 5876479
PMID: 29599150
DOI: 10.1128/genomeA.00003-18

[…] 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 […]

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

[…] 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) []., pagit toolkit [] was used to further improve the quality of the assembly by closing gaps on scaffolds, correcting base errors and generate an annotation of cds based on the reference […]

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

[…] were generated for each strain using mira (http://mira-assembler.sourceforge.net/), spades and newbler (http://www.roche.com/), 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 […]

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 […]

PMCID: 5522941
PMID: 28729274
DOI: 10.1128/genomeA.00674-17

[…] assembled with three different assemblers, including abyss version 1.9 (), soapdenovo2 (), and velvet version 1.2.10 (). finally, qualifying scaffolds from the three assemblies were integrated using cisa version 1.3 (), which showed an outstanding performance compared to the results from each assembler. from the assessment of the de novo assembly using quast version 4.1 (), the assembled draft […]


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CISA institution(s)
Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan

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