ALLPATHS-LG pipeline

ALLPATHS-LG specifications


Unique identifier OMICS_00007
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


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  • person_outline Eric Lander <>

Additional information

Publications for ALLPATHS-LG

ALLPATHS-LG citations

PMCID: 5913678

[…] and sequenced together on a single lane., the ngi trimmed illumina adapter sequences from the raw illumina reads using trimmomatic (bolger et al. 2014) and performed a de novo assembly using allpaths lg (butler et al. 2008) with default parameters. we then performed an additional gap closing step using gapcloser (luo et al. 2012). assembly quality and completeness were assessed using […]

PMCID: 5477391

[…] the illumina hiseqx sequencing platform (scilifelab, sweden). fastqc and trimmomatic tools were used for raw data quality assurance (qa) and quality control (qc), as described previously (5). the allpaths software was used for de novo genome assembly (6). a total of 36.80 m bases were assembled into 341 scaffolds and all are more than 1 kb in length. quast (7) was used to assess assembly […]

PMCID: 5596349

[…] gradient centrifugation to minimize the amount of kinetoplast (mitochondrial) dna. sequencing was performed on illumina hiseq2000 instruments. all illumina sequences were de novo assembled with the allpaths program (59) using the default parameters. pseudochromosome files were generated for scaffold assembly, which was done with abacas2, a currently unpublished successor to abacas (60), using […]

PMCID: 5751062

[…] longstanding interest in differential expression of genes and gene ontology terms specifically between eo and sm (gallant et al. 2012, 2014). , the combined gdna sequence reads were assembled using allpaths-lg to a total base size of 735 mb. the assembly was made up of a total of 4,668 scaffolds with an n50 scaffold length of over 1.7 mb (n50 contig length was 37.6 kb). we refer […]

PMCID: 4939776

[…] of reads with more than 90% of bases with base quality greater than or equal to q20, a total of 28,246,332 shotgun reads (2,85248 mb) and 7,870,684 mate-pair reads (732 mb) were retained. the allpaths-lg whole-genome shotgun assembler (7) was used for the creation of the de novo genome assembly from these short reads. the assembly contained a total of 174 scaffolds with an average read […]

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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