MaqView specifications


Unique identifier OMICS_00889
Name MaqView
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
License GNU General Public License version 3.0
Computer skills Medium
Version 0.1.0
Stability Stable
Maintained Yes



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  • person_outline Mengyao Zhao <>

MaqView in publications

PMCID: 4825977
PMID: 27058864
DOI: 10.1371/journal.pone.0153248

[…] draft sequence of b. peltata was determined by aligning the b. peltata assembled contigs to the cucumis sativus plastid genome [genbank accession: dq865976.1] using the reference-guided assembler maqview(1) (, custom primers () were designed—based on sequence from the draft b. pelata plastid genome—to confirm the junctions of the inverted repeats […]

PMCID: 3734069
PMID: 23940558
DOI: 10.1371/journal.pone.0070307

[…] reference sequence allowing mismatches, thus detecting snps ., snps were identified by samtools (version 0.1.6), which migrated and improved various downstream data processing implemented in maq/maqview such as indexing, pileup, viewer and consensus caller. samtools generated the consensus sequence with the statistical model implemented in maq , . potential pcr duplicates were first removed […]

PMCID: 3091665
PMID: 20701770
DOI: 10.1186/1471-2164-11-469

[…] filtering with the highly stringent criteria as well as aligning onto the 8x scaffold assembly (additional file ). some of the snps were also examined by loading the alignments of short-reads into maqview for visualization (figure ). the flanking 60 bp sequences around the snp position were extracted for the snp array design., to evaluate stringency […]

PMCID: 2885759
PMID: 19906940
DOI: 10.1099/vir.0.015891-0

[…] minimize ambiguities due to the inverted repeats. the reads were aligned with the reference using maq-0.6.8, and the alignment of reads with the reference and read consensus was inspected by using maqview-0.2.1 (; the reference was then improved by reiterative da, employing the whole sequence or substrings thereof (local reiterative da), until the final reference […]

PMCID: 2885757
PMID: 19553388
DOI: 10.1099/vir.0.013250-0

[…] that had originally replaced ul/b′., the illumina data were derived from whole cell dna extracted from human fetal fibroblasts infected with atcc vr-977, and assembled and viewed using maq and maqview (; a total of 47.1 % of the 5 079 235 sequences (50 nt each) aligned with the derived varl consensus and the coverage was 516 reads per nt. test assemblies using […]

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