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|Alternative names||Mimicking Intelligent Read Assembly, MIRA assembler|
|Interface||Command line interface|
|Restrictions to use||None|
|Biological technology||Illumina, Life Technologies, Pacific Biosciences, Roche|
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- person_outline Bastien Chevreux
Publication for Mimicking Intelligent Read Assembly
Complete genome sequence of native Bacillus cereus strains isolated from intestinal tract of the crab Ucides sp.
[…] re removed using the fastq_quality_filter script from the fastx-toolkit package (http://hannonlab.cshl.edu/fastx_toolkit/). De novo genome assemblies 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 […]
Re Assembly and Analysis of an Ancient Variola Virus Genome
[…] d sequence by using alternative assembly strategies. Our first attempts at assembling the data provided by the Sequence Read Archive (SRP091673), using Cutadapt  to trim Illumina adapters and MIRA (Mimicking Intelligent Read Assembly)  and SPAdes (St. Petersburg genome Assembler)  for assembly, created 56 contigs that could not be resolved by modifying the assembly parameters. However, when […]
Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence
[…] A v4.0.2 followed by CAP3 (Table ). The estimated genome size of ~63.64 Mb was obtained by k-mergenie software with optimal k-mer size of 57 (Figure ). An assembly size of 75.37 Mb was obtained using MIRA assembler having 15281 contigs with N50 value of 26586 bp and largest contig length being 249590 bp. Further this assembly was improved using CAP3 software. Finally, we obtained an assembly of si […]
Draft genome sequencing of the sugarcane hybrid SP80 3280
[…] iridiplantae, resulting in 1,224,061 useful for assembly. Prior to assembly, long reads originating from mitochondria (NC_008360.1) and chloroplast (NC_005878.2) were excluded using mirabait ( http://mira-assembler.sourceforge.net/). Reads longer than 1.5Kbp were assembled using Celera’s WGS Assembler v8.2 , using similar parameters as previously described , except for some of the error parameters […]
Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo
[…] genomes, unite them into a single scaffold, and establish the start of the chromosome. Simba includes three different assembly packages: SPAdes 3.6.0 ; MIRA 3.9.18 (http://sourceforge.net/projects/mira-assembler/); and Newbler 2.9 (http://swes.cals.arizona.edu/maier_lab/kartchner/documentation/index.php/home/docs/newbler). A “best” assembly was selected for each isolate based on having the high […]
Insights into the Psychrophilic and Sea Ice Specific Lifestyle of Marinobacter sp. Strain AC 23: a Genomic Approach
[…] bp chemistry on the Ion Torrent PGM platform (Life Technologies, Inc., USA). A total of 4,149,715 high-quality reads were generated upon sequencing of the genome. De novo assembly was performed using MIRA assembler version 4.0.5 (), resulting in 105 contigs. Functional annotation was performed using the Rapid Annotations using Subsystems Technology (RAST) server (). The RAST tool identified Marino […]
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