leeHom

[…] facility (mcmaster university, hamilton ontario, canada)., 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 […]

[…] 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 […]

[…] were assigned to their original library based on perfect matches to one of the expected index combinations. whenever possible, overlapping paired-end reads were merged into single sequences using leehom () in order to reconstruct full-length molecule sequences. all sequences were aligned to the reference genome of a closely related species (see ) using burrows-wheeler aligner (bwa) () […]

[…] 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 […]

[…] paired-end mode on one lane of an illumina hiseq 2500 platform (rapid mode)., base-calling, adaptor trimming and demultiplexing of reads was performed using a custom pipeline based on freeibis (), leehom () and deml (). demultiplexed reads were mapped using tophat v2.0.14, and fpkm (fragments per kilobase of transcript per million mapped reads) values per gene were quantified using cufflinks […]

[…] 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 […]

[…] facility (mcmaster university, hamilton ontario, canada)., 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 […]

[…] analysis (ycga)., 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 […]

[…] misassemblies as defined in [] were combined and are reported as “total misassemblies”., all algorithms for read merging compared here () are based on overlap detection [–], with the exception of leehom [] and bbmerge, which additionally use adapter-sequence detection; and cope [] and bbmerge, which additionally use kmer counts in non-default modes. all tools were executed as described in ., […]

[…] sequences were trimmed from the ends of reads using cutadapt (), allowing an overlap of only 1 base pair (bp) between the adapter and the read. for paired-end data, adapters were trimmed using leehom (). leehom was run using the --ancientdna option, and paired-end reads that overlapped were merged. for paired-end reads that could not be overlapped, only data from read 1 were used […]