REAPR pipeline

REAPR specifications

Information


Unique identifier OMICS_04068
Name REAPR
Alternative name Recognising Errors in Assemblies using Paired Reads
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Recognising Errors in Assemblies using Paired Reads

REAPR IN pipelines

 (4)
2018
PMCID: 5936940
PMID: 29765675
DOI: 10.1098/rsos.172212

[…] control were contiguated (aligned, ordered and oriented) using the extensively finished l. braziliensis m2904 reference with abacas [59]. the output was split into 35 pseudo-chromosomes and reapr [60] broke scaffolds at possible misassemblies to assess contiguation accuracy. the pseudo-chromosome lengths of each sample approximated the length of each corresponding l. braziliensis m2904 […]

2017
PMCID: 5905499
PMID: 29253216
DOI: 10.1093/gigascience/gix125

[…] genome sequence, homologous sequences can assemble separately or merge. moreover, unresolved repeat structures in the assembly might also contribute heavily to this issue. structural errors in reapr were likely called at the boundaries of these regions. the final genome assembly after reapr breaks had 19 319 sequences of a length of 1 kbp or longer, with 576 829 188 bp. the n50 size […]

2017
PMCID: 5905499
PMID: 29253216
DOI: 10.1093/gigascience/gix125

[…] repeat structures in the assembly might also contribute heavily to this issue. structural errors in reapr were likely called at the boundaries of these regions. the final genome assembly after reapr breaks had 19 319 sequences of a length of 1 kbp or longer, with 576 829 188 bp. the n50 size of scaffolds dropped from 97 344 kb (l50 = 1792) to 71 491 bp (l50 = 2379). the number of remaining […]

2015
PMCID: 4501334
PMID: 26175406
DOI: 10.7554/eLife.06974.033

[…] 2010), using the amplification-free library. furthermore, sequencing gaps were closed, using image (tsai et al., 2010) with the amplification-free library. the assembly was quality-controlled using reapr (hunt et al., 2013), breaking the contigs at possible miss-assemblies, using the mate pair libraries. this was followed by another scaffolding step. we systematically removed 620 scaffolds […]

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