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ALLPATHS-LG specifications


Unique identifier OMICS_00007
Alternative name ALLPATHS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some files containing sequenced reads, their quality scores and information concerning their pairing.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline David Jaff
  • person_outline Eric Lander

Additional information

Publications for ALLPATHS-LG

ALLPATHS-LG citations


Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose utilizing derivatives 8b and 2032

Biotechnol Biofuels
PMCID: 5930841
PMID: 29743953
DOI: 10.1186/s13068-018-1116-x

[…] vided 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 ( [, ] using the trimmed/normalized short-pair reads and the NextClip processed mate-pair reads. Assembly statistics were colle […]


Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044
call_split See protocol

[…] ersion 1.3.1) [] with default parameters were used to trim sequencing reads. Genome assembly into contigs was performed using MaSuRCA (version 2.3.2) [] with settings based on the instruction manual. ALLPATHS-LG (ALLPATHS-LG, RRID:SCR_010742, version 49722) [], Newbler (version 2.9) [] both with default parameters, JR (version 1.0.4; parameters: “-minOverlap 60 -maxOverlap 90 -ratio 0.3”) [], SGA […]


Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen fixing rhizobium symbioses

Proc Natl Acad Sci U S A
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] 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 def […]


Complete Genome Sequence of Agrobacterium tumefaciens 1D1609

Genome Announc
PMCID: 5908930
PMID: 29674541
DOI: 10.1128/genomeA.00253-18

[…] as used to generate 301-bp reads from one paired-end library (∼550-bp insert, 11,564,340 reads) and one mate pair library (∼4,100-bp insert, 8,219,766 reads). The de novo assembly was performed using AllPaths-LG (). The initial draft assembly was iteratively improved using PAGIT (). In each iteration, the Illumina reads were mapped to the assembly using Burrows-Wheeler Aligner (BWA) (), programmat […]


Complete Genome Sequence of Spiroplasma floricola 23 6T (ATCC 29989), a Bacterium Isolated from a Tulip Tree (Liriodendron tulipifera L.)

Genome Announc
PMCID: 5908944
PMID: 29674553
DOI: 10.1128/genomeA.00302-18

[…] generate raw reads from one paired-end library (∼283-bp insert, ∼416-fold coverage) and one mate-pair library (∼4,000-bp insert, ∼476-fold coverage). The initial de novo assembly was performed using ALLPATHS-LG release 52188 (). Subsequently, PAGIT version 1 () was used to assist an iterative process for improving the assembly. For each iteration, the raw reads were mapped to the assembly using B […]


A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

BMC Genomics
PMCID: 5902842
PMID: 29661190
DOI: 10.1186/s12864-018-4656-3
call_split See protocol

[…] e (240 and 160 bases, respectively). The libraries yielded 169,008,438 and 170,367,691 read pairs, respectively. Prior to assembly, reads were error-corrected using the error correction tool from the ALLPATHS-lg assembler [] yielding 159,232,897 and 167,054,602 corrected read pairs, respectively. These reads were also used to estimate genome size using both preQC ( […]


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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)
Supported 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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