AlignerBoost protocols

View AlignerBoost computational protocol

AlignerBoost statistics

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Tool usage distribution map

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Associated diseases

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AlignerBoost specifications

Information


Unique identifier OMICS_13083
Name AlignerBoost
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data DNA-seq and RNA-seq datasets at various
Input format SAM, BAM, BED, GFF
Output data NGS read mapping
Output format BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Source code URL https://codeload.github.com/Grice-Lab/AlignerBoost/zip/master
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Qi Zheng <>

Publication for AlignerBoost

AlignerBoost in pipeline

2018
PMCID: 5789709
PMID: 29378633
DOI: 10.1186/s40168-018-0404-9

[…] see additional file : table s1 for sample summaries) of good quality (additional file : figure s1a). reads were mapped to the mouse reference genome using the star aligner [], in conjunction with alignerboost []. of reads that aligned to the mouse reference genome, an average of 88% of reads per sample were assigned to a feature (additional file : figure s1b), and the majority mapped […]


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AlignerBoost in publications

 (2)
PMCID: 5789709
PMID: 29378633
DOI: 10.1186/s40168-018-0404-9

[…] sequenced on the illumina hiseq 2000 to obtain 100 bp paired-end reads per skin sample., transcripts were aligned to the mouse reference genome grcm38.p4 v9 [], using star [] in conjunction with alignerboost [], and specifying a seed length of 25, 4% seed mismatch, 0% seed indels, 8% all mismatch, and 3% all indels. reads mapping to numbered and sex chromosomes were retained. read counts […]

PMCID: 5846869
PMID: 29568413
DOI: 10.1007/s13258-017-0621-9

[…] option (dna-based paired-end sequencing allowing mismatches, indels, gaps) and the quality awareness of the tools (utilization of mapping quality). tools that were not compatible with our system, alignerboost (zheng and grice ) and cora (yorukoglu et al. ), were excluded from the list., the eight selected tools and their basic features are listed in table . the number of citations […]


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AlignerBoost institution(s)
Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
AlignerBoost funding source(s)
The National Institutes of Health, National Institutes of Arthritis and Musculoskeletal and Skin Disease (Grant R01 AR066663); the National Institute of Nursing Research (Grant R01NR015639); the Department of Dermatology at University of Pennsylvania

AlignerBoost review

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caseyb

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Great support for many different DNA aligner tools