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ALE specifications


Unique identifier OMICS_04067
Name ALE
Alternative name Assembly Likelihood Estimator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Python
Computer skills Advanced
Stability No
Maintained No




No version available

Publication for Assembly Likelihood Estimator

ALE citations


Deeply sourced formate fuels sulfate reducers but not methanogens at Lost City hydrothermal field

Sci Rep
PMCID: 5768773
PMID: 29335466
DOI: 10.1038/s41598-017-19002-5

[…] subsequently mapped to contigs with fdhA or fdhB sequences, and these reads were re-assembled with a kmer of 61. Several assembly strategies and parameters were tested and compared with MetaQuast and ALE. The Prokka pipeline was used for gene prediction and functional annotation. The arguments–metagenome and–proteins were used with Prokka v.1.12 to indicate that genes should be predicted with the […]


Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus

PMCID: 5705806
PMID: 29202045
DOI: 10.1128/mSphere.00511-17

[…] novo assembly (). We chose to compare assemblies from SPAdes (), MaSurCA (), and Velvet (). KmerGenie () was used to select kmer sizes for assembly. iMetAMOS uses FastQC, QUAST (), REAPR (), LAP (), ALE (), FreeBayes (), and CGAL () to evaluate the quality of reads and assemblies. We also used Kraken () to detect potential contamination in sequence data. For all newly assembled isolates (43, SSC0 […]


Reference guided de novo assembly approach improves genome reconstruction for related species

BMC Bioinformatics
PMCID: 5681816
PMID: 29126390
DOI: 10.1186/s12859-017-1911-6

[…] e scaffolds. We also applied two evaluation tools which are independent of any reference sequence, instead they use read alignments for assembly evaluations: the generic assembly likelihood framework ALE [] and the universal genome assembly evaluation tool REAPR v1.0.18 []. ALE scores were estimated based on the alignments of the 200 and 400 bp insertion paired-end libraries against the scaffolds. […]


Toward Universal Forward Genetics: Using a Draft Genome Sequence of the Nematode Oscheius tipulae To Identify Mutations Affecting Vulva Development

PMCID: 5560785
PMID: 28630114
DOI: 10.1534/genetics.117.203521
call_split See protocol

[…] d read set was estimated using KmerGenie (). Nine different assemblers () were used to generate preliminary assemblies and these were assessed using basic metrics, correctness of read alignment using ALE () and REAPR (), and biological completeness using Core Eukaryotic Genes Mapping Appoach (CEGMA) () and direct identification of ribosomal RNA genes and mitochondrial genome sequences. SPAdes () o […]


A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions

BMC Genomics
PMCID: 5414186
PMID: 28464822
DOI: 10.1186/s12864-017-3723-5

[…] ands were used to convert the Bowtie2 SAM outputs to BAM format. The Picard [] (version 2.1.0) ‘MarkDuplicates’ program was run on each of these Bowtie2 alignments with ‘REMOVE_DUPLICATES = true’.The Assembly Likelihood Estimator (ALE) [] was then run on each of these filtered BAM files to generate likelihood statistics for each candidate Canu and FALCON de novo assembly for each Illumina library. […]


Virome Assembly and Annotation: A Surprise in the Namib Desert

Front Microbiol
PMCID: 5253355
PMID: 28167933
DOI: 10.3389/fmicb.2017.00013

[…] ds back to the assembled contigs using Bowtie2 v-2.2.6 (Langmead and Salzberg, ), selecting end-to-end matches (–no-1 mm-upfront switched on) and reporting multiple alignments (-k 3); and (3) running ALE (Clark et al., ) on all assembled datasets to compare the performance of the different assemblers. Genomes were considered “recovered” if they were reassembled into one sequence. […]


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ALE institution(s)
Center for Applied Mathematics, Cornell University, Ithaca, NY, USA

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