As high-throughput sequencing platforms produce longer and longer reads, sequences generated from short inserts, such as those obtained from fossil and degraded material, are increasingly expected to contain adapter sequences. Efficient adapter trimming algorithms are also needed to process the growing amount of data generated per sequencing run. We introduce AdapterRemoval v2, a major revision of AdapterRemoval v1, which introduces (i) striking improvements in throughput, through the use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support, (ii) the ability to handle datasets containing reads or read-pairs with different adapters or adapter pairs, (iii) simultaneous demultiplexing and adapter trimming, (iv) the ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets, and (v) native gzip and bzip2 support. We show that AdapterRemoval v2 compares favorably with existing tools, while offering superior throughput to most alternatives examined here, both for single and multi-threaded operations.

/pdf/adapterremoval-v2-rapid-adapter-trimming-identification-and-1ml1rcsk5u.pdf

AdapterRemoval v2: rapid adapter trimming, identification, and read merging.

Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls and the leading causal artifacts still remain unclear even given the great efforts in the evaluation of variant calling methods.

Results: We made 10 single nucleotide polymorphism and INDEL call sets with two read mappers and five variant callers, both on a haploid human genome and a diploid genome at a similar coverage. By investigating false heterozygous calls in the haploid genome, we identified the erroneous realignment in low-complexity regions and the incomplete reference genome with respect to the sample as the two major sources of errors, which press for continued improvements in these two areas. We estimated that the error rate of raw genotype calls is as high as 1 in 10–15 kb, but the error rate of post-filtered calls is reduced to 1 in 100–200 kb without significant compromise on the sensitivity.

Availability and implementation: BWA-MEM alignment and raw variant calls are available at http://bit.ly/1g8XqRt scripts and miscellaneous data at https://github.com/lh3/varcmp.

Contact: gro.etutitsnidaorb@ilgneh

Supplementary information: Supplementary data are available at Bioinformatics online.

Toward better understanding of artifacts in variant calling from high-coverage samples

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.

/pdf/assembly-and-diploid-architecture-of-an-individual-human-5gk33506ex.pdf

Assembly and diploid architecture of an individual human genome via single-molecule technologies

Autism Spectrum Disorder (ASD) demonstrates high heritability and familial clustering, yet the genetic causes remain only partially understood as a result of extensive clinical and genomic heterogeneity. Whole-genome sequencing (WGS) shows promise as a tool for identifying ASD risk genes as well as unreported mutations in known loci, but an assessment of its full utility in an ASD group has not been performed. We used WGS to examine 32 families with ASD to detect de novo or rare inherited genetic variants predicted to be deleterious (loss-of-function and damaging missense mutations). Among ASD probands, we identified deleterious de novo mutations in six of 32 (19%) families and X-linked or autosomal inherited alterations in ten of 32 (31%) families (some had combinations of mutations). The proportion of families identified with such putative mutations was larger than has been previously reported; this yield was in part due to the comprehensive and uniform coverage afforded by WGS. Deleterious variants were found in four unrecognized, nine known, and eight candidate ASD risk genes. Examples include CAPRIN1 and AFF2 (both linked to FMR1, which is involved in fragile X syndrome), VIP (involved in social-cognitive deficits), and other genes such as SCN2A and KCNQ2 (linked to epilepsy), NRXN1, and CHD7, which causes ASD-associated CHARGE syndrome. Taken together, these results suggest that WGS and thorough bioinformatic analyses for de novo and rare inherited mutations will improve the detection of genetic variants likely to be associated with ASD or its accompanying clinical symptoms.

https://www.cell.com/ajhg/pdf/S0002-9297(13)00281-4.pdf

Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing

Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its Mexican center of origin was low, and one scenario held that a single strain, US-1, had dominated the global population for 150 years; this was later challenged based on DNA analysis of historical herbarium specimens. We have compared the genomes of 11 herbarium and 15 modern strains. We conclude that the 19th century epidemic was caused by a unique genotype, HERB-1, that persisted for over 50 years. HERB-1 is distinct from all examined modern strains, but it is a close relative of US-1, which replaced it outside of Mexico in the 20th century. We propose that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species' center of diversity.

DOI: http://dx.doi.org/10.7554/eLife.00731.001

/pdf/the-rise-and-fall-of-the-phytophthora-infestans-lineage-that-oh22d6r5zr.pdf

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine.

M otivation: The next generation high-throughput sequencing technologies, especially from Illumina, have been widely used in re- sequencing and de novo assembly studies. However, there is no existing software that can simulate Illumina reads with real error and quality distributions and coverage bias yet, which is very useful in relevant software development and study designing of sequencing projects. Results: We provide a software package, pIRS (profile based Illumina pair-end Reads Simulator), which simulates Illumina reads with empirical Base-Calling and GC%-depth profiles trained from real re-sequencing data. The error and quality distributions as well as coverage bias patterns of simulated reads using pIRS fit the properties of real sequencing data better than existing simulators. In addition, pIRS also comes with a tool to simulate the heterozygous diploid genomes. Availability: pIRS is written in C++ and Perl, and is freely available at ftp://ftp.genomics.org.cn/pub/pIRS/ .

/pdf/pirs-profile-based-illumina-pair-end-reads-simulator-2syn6u68xe.pdf

pIRS: Profile-based Illumina pair-end reads simulator

We present a new approach to indel calling that explicitly exploits that indel differences between a reference and a sequenced sample make the mapping of reads less efficient. We assign all unmapped reads with a mapped partner to their expected genomic positions and then perform extensive de novo assembly on the regions with many unmapped reads to resolve homozygous, heterozygous, and complex indels by exhaustive traversal of the de Bruijn graph. The method is implemented in the software SOAPindel and provides a list of candidate indels with quality scores. We compare SOAPindel to Dindel, Pindel, and GATK on simulated data and find similar or better performance for short indels ( 5 bp), while still providing many more candidate indels than other approaches.

/pdf/soapindel-efficient-identification-of-indels-from-short-3u7x3uy284.pdf

Jianliang Lu

Papers

pIRS: Profile-based Illumina pair-end reads simulator

SOAPindel: Efficient identification of indels from short paired reads