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Protocols

sabre specifications

Information


Unique identifier OMICS_01090
Name sabre
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


sabre citations

 (8)
library_books

Genotyping of Plasmodiophora brassicae reveals the presence of distinct populations

2018
BMC Genomics
PMCID: 5902848
PMID: 29661147
DOI: 10.1186/s12864-018-4658-1

[…] orrent Suite v4.4.3 (Life Technologies), which removed low quality sequences and removed the ion torrent adapters and low quality 3′ ends. Reads were demultiplexed based on the barcode sequence using Sabre (https://github.com/najoshi/sabre). As the P. brassicae DNA would likely be contaminated with some host DNA, the amount of host contamination was determined and removed by alignment against the […]

library_books

A comparison of genotyping by sequencing analysis methods on low coverage crop datasets shows advantages of a new workflow, GB eaSy

2017
BMC Bioinformatics
PMCID: 5745977
PMID: 29281959
DOI: 10.1186/s12859-017-2000-6

[…] fined directory structure and naming input files according to a specific convention, the user issues a single command that runs the entire pipeline. IGST demultiplexes and cleans barcoded reads using Sabre (https://github.com/najoshi/sabre), aligns demultiplexed reads to the reference genome using BWA-ALN [], converts the aligned sequences to BAM format using SAMtools [], and identifies SNPs using […]

call_split

Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass

2017
Sci Rep
PMCID: 5472636
PMID: 28620209
DOI: 10.1038/s41598-017-03232-8
call_split See protocol

[…] le was used to trim reads when the average quality score in a sliding window (of 20 bp) fell below a phred score of 20, and reads shorter than 40 bp were discarded. The reads were demultiplexed using sabre and data from each sample was aligned to the perennial ryegrass reference genome using BWA. The Genome Analysis Tool Kit (GATK) was used to identify putative variants in the complete population […]

call_split

Stressor exposure has prolonged effects on colonic microbial community structure in Citrobacter rodentium challenged mice

2017
Sci Rep
PMCID: 5366811
PMID: 28344333
DOI: 10.1038/srep45012
call_split See protocol

[…] Forward and reverse ends were demultiplexed using Sabre (website: http://github.com/najoshi/sabre), with 1 allowed barcode mismatch. Barcodes were removed and sequences were trimmed for equal lengths using FastX Trimmer (website: http://hannonlab.csh […]

library_books

The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry

2017
Sci Rep
PMCID: 5240624
PMID: 28094805
DOI: 10.1038/srep40728

[…] trim reads when the average quality score in a sliding window (of 20 bp) fell below a phred score of 20. At this point reads shorter than 40 bp were also discarded. The reads were demultiplexed using sabre (https://github.com/najoshi/sabre), and all reads originating from the same sample were combined. Reads were aligned to the draft B. vulgaris assembly using BWA, and the Genome Analysis Tool Kit […]

library_books

Markers associated with heading and aftermath heading in perennial ryegrass full sib families

2016
BMC Plant Biol
PMCID: 4947259
PMID: 27422157
DOI: 10.1186/s12870-016-0844-y

[…] [] was used to trim reads when the average quality score in a sliding window (of 20 bp) fell below a phred score of 20, and reads shorter than 40bp were discarded. The reads were demultiplexed using sabre [] and data from each sample was aligned to the perennial ryegrass reference genome [] using BWA []. The Genome Analysis Tool Kit (GATK) [] was used to identify putative variants across the full […]

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