PALEOMIX protocols

PALEOMIX specifications

Information


Unique identifier OMICS_03749
Name PALEOMIX
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data One or more FASTQ files containing sequencing reads produced by NGS platforms, one or more FASTA files containing the reference sequences against which the FASTQ files are to be mapped
Input format FASTQ, FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for PALEOMIX

PALEOMIX IN pipelines

 (3)
2017
PMCID: 5492679
PMID: 28662691
DOI: 10.1186/s12864-017-3883-3

[…] we built a custom processing pipeline to ensure that all the data were processed using the same tools and were subject to the same quality control and filtering. we built our pipeline on the paleomix pipeline developed by schubert et al. [48]. the various parts of our processing pipeline are detailed below., each sample used in this study was mapped against both the dog reference genome […]

2017
PMCID: 5492679
PMID: 28662691
DOI: 10.1186/s12864-017-3883-3

[…] processing pipeline are detailed below., each sample used in this study was mapped against both the dog reference genome (canfam3.1) [35] and the de-novo assembled wolf reference genome. we used the paleomix pipeline to map the short reads from the samples to both the genomes. specifically, we used bwa-0.7.10 (the aln algorithm) [49] to map the reads to the genome. after the initial alignment […]

2017
PMCID: 5544389
PMID: 28757201
DOI: 10.1016/j.ajhg.2017.06.013

[…] to published protocols without uracil-dna glycosylase treatment.18, 19, 20, 21 we sequenced the libraries on an illumina hiseq 2500 using 2× 75 bp reads and processed the sequences using the paleomix pipeline.22 we retained reads ≥30 bp and collapsed pairs with minimum overlap of 15 bp, allowing a mismatch rate of 0.06 between the pairs. we mapped the merged sequences to the hs37d5 […]

PALEOMIX institution(s)
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Biomedical Informatics and Computational Biology Graduate Program, University of Minnesota Rochester, Chinahester, MN, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
PALEOMIX funding source(s)
This work was supported by the Danish Council for Independent Research, Natural Sciences (FNU); the Danish National Research Foundation (DNRF94); a Marie-Curie Career Integration grant (FP7 CIG-293845); the Lundbeck foundation (R52-A5062).

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