leeHom

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]