ALLPATHS-LG protocols

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ALLPATHS-LG specifications

Information


Unique identifier OMICS_00007
Name ALLPATHS-LG
Alternative name ALLPATHS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Eric Lander <>

Additional information


http://software.broadinstitute.org/allpaths-lg/blog/?page_id=2

Publications for ALLPATHS-LG

ALLPATHS-LG in pipelines

 (58)
2018
PMCID: 5886536
PMID: 29621340
DOI: 10.1371/journal.pone.0195461

[…] database []. the repbase sequences originated from the salmoniformes family, and excluded simple repeats (downloaded january 13, 2017). repeatmodeler v1.0.8 [] was also used together with the allpaths-lg initial assembly in a de novo approach, which identified 1,124 repetitive sequences., the repetitive sequences were then aligned to the chinook genome with blastn v2.2.28+ []. a wordsize […]

2018
PMCID: 5886536
PMID: 29621340
DOI: 10.1371/journal.pone.0195461

[…] from each of the different sequencing libraries. roughly 73x coverage from two paired-end libraries and three mate-pair libraries was used to generate the initial genome assembly with the allpaths-lg program. the contig n50 for the initial assembly was 14.6 kb, and the scaffold n50 was 1.086 mb., after adding the pacbio data using the pbjelly software, the contig n50 increased […]

2018
PMCID: 5897751
PMID: 29681895
DOI: 10.3389/fmicb.2018.00676

[…] scientific, usa). sequencing was performed by illumina miseq with a 2 × 300 bp paired-end (insert ~550 bp) and a 2 × 300 bp mate-pair (insert ~3000 bp) runs. genome assembly was performed with allpaths-lg v50960 (ribeiro et al., ) using the default parameters. genome completeness and purity was checked with the checkm v0.9.6 software suite (parks et al., ) and annotation of the resulting […]

2018
PMCID: 5913678
PMID: 29528428
DOI: 10.1093/molbev/msy037

[…] were multiplexed and sequenced together on a single lane., the ngi trimmed illumina adapter sequences from the raw illumina reads using trimmomatic () and performed a de novo assembly using allpaths lg () with default parameters. we then performed an additional gap closing step using gapcloser (). assembly quality and completeness were assessed using buscov2 () using both the eukaryote […]

2017
PMCID: 5301235
PMID: 28186206
DOI: 10.1038/srep42444

[…] remove adaptor contaminations and low quality sequences with trimmomatic (version 3.2). the clean data were subjected to error correction using the error correction module (errorcorrectreads.pl) in allpaths-lg with the parameters of “phred_encoding = 33 ploidy = 1”. genome size was estimated during the procedure of error correction., corrected sequences were subjected to k-mer counting using […]


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ALLPATHS-LG in publications

 (465)
PMCID: 5930841
PMID: 29743953
DOI: 10.1186/s13068-018-1116-x

[…] by the trinity software package [] using kmer_size = {21, 23, 24, 25, 27, 29} and max_cov = {10,15, 25, 35, 50}. for each setting of kmer_size and max_cov, a genome assembly was generated using allpaths-lg v.44837 (http://software.broadinstitute.org/allpaths-lg/blog/) [, ] using the trimmed/normalized short-pair reads and the nextclip processed mate-pair reads. assembly statistics […]

PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] using a large number of tools at different stages for the assembly of the mikado pheasant genome. while conducting the genome assembly, we used not only masurca but also assembly tools such as allpaths-lg [], jr [], newbler [], sga [], and soapdenovo []. all of these assembly tools produced similar draft genome sizes, and masurca and sga also showed similar results in terms of the n50 […]

PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] hybrid plant h9 was propagated in vitro (, ). the karyotype of the selected plants was determined according to geurts and de jong ()., cleaned dna sequencing reads were de novo assembled by using allpaths-lg (release 48961) (). after filtering of any remaining adapters and contamination, contigs were scaffolded with two rounds of sspace-standard (v3.0) () with the mate-pair libraries using […]

PMCID: 5932639
PMID: 29755354
DOI: 10.3389/fphar.2018.00419

[…] low quality reads (https://github.com/agordon/fastx_toolkit). sequencing data was first assembled using velvet v. 1.2.07 (zerbino and birney, ), and the resulted contigs were then scaffolded with allpaths v. r46652 (butler et al., )., the annotation of the strain yhl was performed using the national center for biotechnology information (ncbi) prokaryotic genomes automatic annotation pipeline […]

PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] ≤8); (2) reads with ns >10% of the read length; (3) reads with adapter contamination; and (4) duplicated reads caused by pcr during library construction. filtered data were assembled using allpaths-lg (version 44080), where overlapping paired-end reads with an insert size of 230 nucleotides were used as fragment libraries, and all other libraries (>230 nucleotide insert size) […]


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ALLPATHS-LG institution(s)
Broad Institute of MIT and, Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA
ALLPATHS-LG funding source(s)
This work was carried out with the aid of federal funds provided by the National Institutes of Health, Department of Health and Human Services, via Grants U54HG003067 and R01HG003474 through the National Human Genome Research Institute and Contract HHSN2722009000018C through the National Institute of Allergy and Infectious Diseases.

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