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Protocols

Isaac Genome Alignment Software specifications

Information


Unique identifier OMICS_00289
Name Isaac Genome Alignment Software
Alternative name Isaac aligner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://github.com/sequencing/isaac_aligner/wiki/Isaac-aligner

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  • person_outline Come Raczy

Publication for Isaac Genome Alignment Software

Isaac Genome Alignment Software citations

 (12)
library_books

CRISPR LbCpf1 prevents choroidal neovascularization in a mouse model of age related macular degeneration

2018
Nat Commun
PMCID: 5945874
PMID: 29748595
DOI: 10.1038/s41467-018-04175-y

[…] Covaris system and ligated with adapters for library formation. DNA libraries were subjected to whole-genome sequencing using an Illumina HiSeq X Ten Sequencer at Macrogen (South Korea),. We used the Isaac aligner to generate a Bam file using the following parameters: ver. 01.14.03.12; Mouse genome reference, mm10 from UCSC; Base quality cutoff, 15; Keep duplicate reads, yes; Variable read length […]

library_books

Identification of rare sequence variation underlying heritable pulmonary arterial hypertension

2018
Nat Commun
PMCID: 5897357
PMID: 29650961
DOI: 10.1038/s41467-018-03672-4

[…] Sequencing reads were pre-processed by Illumina with Isaac Aligner and Variant Caller (v2, Illumina Inc.) using human genome assembly GRCh37 as reference. Variants were normalised, merged into multi-sample VCF files by chromosome using the gVCF aggregat […]

library_books

Chromothripsis and ring chromosome 22: a paradigm of genomic complexity in the Phelan McDermid syndrome (22q13 deletion syndrome)

2018
J Med Genet
PMCID: 5869459
PMID: 29378768
DOI: 10.1136/jmedgenet-2017-105125

[…] turer’s protocol. We obtained an average coverage of 42X in the father’s sample and 37X in the proband’s sample. Reads from the fastq files were mapped to the human reference genome GRCh37/hg19 using Isaac Genome Alignment Software (V.iSAAC-03.16.06.06). Coverage graphs were performed plotting the average coverage of 1000 bp windows sliding over the whole chromosome length, in order to identify la […]

library_books

Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole genome sequencing as a first tier genetic test

2017
Genet Med
PMCID: 5895460
PMID: 28771251
DOI: 10.1038/gim.2017.119

[…] ng and data analysis were performed using BCL2FASTQ, and data were analyzed using Illumina HiSeq Analysis Software (HAS; version 2-2.5.55.1311). Reads were mapped to the hg19 reference sequence using Isaac Genome Alignment Software (SAAC00776.15.01.27) (Illumina) and SNVs and small indel variants were called using Starling (Isaac Variant Caller; version 2.1.4.2). WGS data will be deposited in the […]

call_split

GNAO1 encephalopathy

2017
PMCID: 5362187
PMID: 28357411
DOI: 10.1212/NXG.0000000000000143
call_split See protocol

[…] of the National Institute for Health Research Bioresource Rare Disease Project. A minimum coverage of 15X (95% of the genome) was obtained, with an average coverage of ∼30X. Reads were aligned using Isaac aligner (version 01.14) (Illumina Inc., Great Chesterford, UK) and mapped against the GRCh37 hg19 human assembly. Single nucleotide variants and insertions/deletions were identified using Isaac […]

call_split

In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni

2017
Nat Commun
PMCID: 5473640
PMID: 28220790
DOI: 10.1038/ncomms14500
call_split See protocol

[…] ested DNA was fragmented using the Covaris system and ligated with adaptors for library formation. DNA libraries were subjected to WGS using an Illumina HiSeq X Ten Sequencer at Macrogen. We used the Isaac aligner to generate a Bam file using the following parameters: ver. 01.14.03.12; Human genome reference, hg19 from UCSC (original GRCh37 from NCBI, Feb. 2009), Mouse genome reference, mm10 from […]


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Isaac Genome Alignment Software institution(s)
Illumina United Kingdom, Chesterford Research Park, Essex, UK ; Illumina, Inc., San Diego, CA, USA

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