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leeHom specifications


Unique identifier OMICS_05254
Name leeHom
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1.5
Stability Stable
Maintained Yes


No version available



  • person_outline Gabriel Renaud
  • person_outline Janet Kelso

Publication for leeHom

leeHom citations


Contrasting maternal and paternal genetic variation of hunter gatherer groups in Thailand

Sci Rep
PMCID: 5784115
PMID: 29367746
DOI: 10.1038/s41598-018-20020-0

[…] atform, generating paired-end reads of 125 bp length. Standard Illumina base-calling was performed using Bustard. We trimmed Illumina adapters and merged completely overlapping paired sequences using leeHOM and de-multiplexed the pooled sequencing data using deML.The sequencing data were aligned against the human reference genome hg19 using BWA’s aln algorithm and all sequence pairs that aligned t […]


The paradox of HBV evolution as revealed from a 16th century mummy

PLoS Pathog
PMCID: 5754119
PMID: 29300782
DOI: 10.1371/journal.ppat.1006750
call_split See protocol

[…] Reads were demultiplexed using CASAVA-1.8.2 (Illumina, San Diego, California), then adapters were trimmed and reads merged using leeHom [] with aDNA specific settings (—ancientdna). These processed reads were mapped to an appropriate reference genome (HBV genotype D3, GenBank accession X65257; revised Cambridge Reference Sequen […]


Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico

Sci Rep
PMCID: 5741722
PMID: 29273718
DOI: 10.1038/s41598-017-18356-0

[…] Sequence reads were processed using a bioinformatics pipeline optimized for ancient DNA analysis. Post-capture paired reads were merged and adapters were trimmed with the program leeHom using the ancient DNA flag. The reads were mapped to the rCRS using a modified version Burrows Wheeler Aligner (-n 0.01, -o 2, -l 16500) (https://github.com/mpieva/network-aware-bwa). Reads wer […]


BBMerge – Accurate paired shotgun read merging via overlap

PLoS One
PMCID: 5657622
PMID: 29073143
DOI: 10.1371/journal.pone.0185056

[…] ear-perfect scaling in these tests, and are expected to continue scaling past 32 threads if run on a system with more CPU cores (). FLASH scaled linearly to 6 threads, at which point speed plateaued. leeHom scaled to a peak at 4 threads, after which speed slightly declined. USEARCH also reached a peak at ~4 threads, but did not scale as well; 4-threaded speed was only 150% of single-threaded speed […]


A fourth Denisovan individual

Sci Adv
PMCID: 5501502
PMID: 28695206
DOI: 10.1126/sciadv.1700186

[…] ase calling was carried out using freeIbis () and Bustard (Illumina) for HiSeq and MiSeq runs, respectively. Adapter sequences were removed and overlapping forward and reverse reads were merged using leeHom (). Sequences that did not perfectly match the expected barcode combinations were discarded. For each library, sequences originating from different sequencing runs were combined using SAMtools […]


A molecular portrait of maternal sepsis from Byzantine Troy

PMCID: 5224923
PMID: 28072390
DOI: 10.7554/eLife.20983.043

[…] e abundance, coverage, and authenticity of our ancient reads, we ran a subset of analyses using slightly more stringent criteria. CASAVA (RRID:SCR_001802) processed reads were trimmed and merged with leeHom () (RRID:SCR_002710) using its ancient DNA parameter (--ancientdna). We restricted reads from the UDG-treated shotgun nodule libraries (Nod1_1h-UDG and Nod2-UDG) to those of minimum 35 bp lengt […]


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leeHom institution(s)
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
leeHom funding source(s)
Supported by the Max Planck Society and NSERC for PGS Doctoral scholarship.

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