ALLPATHS-LG specifications

Information


Unique identifier OMICS_00007
Name ALLPATHS-LG
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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Documentation


Maintainer


  • person_outline Eric Lander <>

Additional information


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

ALLPATHS-LG articles

ALLPATHS-LG citations

 (6)
2016
PMCID: 4974330

[…] the resulting sequencing data included 3.51-mb paired-end and 5.51-mb mate-pair reads, with average read lengths of approximately 250 and 2,000 bp, respectively. genomic sequence assembly using allpaths-lg version 46449 (7) produced four scaffolds composed of 23 contigs and a 7.97-mb draft genome sequence at a 166-fold coverage from both the paired-end and mate-pair libraries. the length […]

2016
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 […]

2016
PMCID: 4939777

[…] filtering, reads with more than 90% of bases with base quality greater than or equal to q20, a total of 28,200,910 shotgun reads (2,848 mb) and 8,857,004 mate-pair reads (815 mb), were retained. the allpaths-lg whole-genome shotgun assembler (6) was used for the creation of the de novo genome assembly from these short reads. the assembly contained a total of 164 scaffolds with an average read […]

2014
PMCID: 4218959

[…] total raw sequence coverage of illumina reads was ~95 × (short insert paired-end reads, 3, 8 and 40 kb mate-paired libraries, supplementary data 1). the combined sequence reads were assembled using allpaths software59 and the assembled coverage was 70 × . this draft assembly was referred to as astyanax mexicanus 1.0.2. this assembly has been gap filled with a version of image60, modified […]

2014
PMCID: 4183885

[…] 6,818,142 reads), and the illumina hiseq 2000 platform was used to generate 126-bp reads from one mate-pair library (~4.1-kb insert, 6,962,414 reads). the de novo assembly was performed using allpaths-lg release 42781 (9). the initial assembly was iteratively improved by mapping the raw reads to the contigs using burrows-wheeler aligner (bwa) version 0.6.2 (10), programmatically checked […]

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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