Abstract
Motivation
Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in ...length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.
Results
Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment.
Availability and implementation
https://github.com/lh3/minimap2
Supplementary information
Supplementary data are available at Bioinformatics online.
Abstract
Summary
We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly repetitive ...regions and align through insertions or deletions up to 100 kb by default, addressing major weakness in minimap2 v2.18 or earlier.
Availability and implementation
https://github.com/lh3/minimap2.
Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10 kb in length, which have enabled high-quality genome assembly at an affordable ...cost. However, at present, long reads have an error rate as high as 10-15%. Complex and computationally intensive pipelines are required to assemble such reads.
We present a new mapper, minimap and a de novo assembler, miniasm, for efficiently mapping and assembling SMRT and ONT reads without an error correction stage. They can often assemble a sequencing run of bacterial data into a single contig in a few minutes, and assemble 45-fold Caenorhabditis elegans data in 9 min, orders of magnitude faster than the existing pipelines, though the consensus sequence error rate is as high as raw reads. We also introduce a pairwise read mapping format and a graphical fragment assembly format, and demonstrate the interoperability between ours and current tools.
https://github.com/lh3/minimap and https://github.com/lh3/miniasm
hengli@broadinstitute.org
Supplementary data are available at Bioinformatics online.
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be ...easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty.
Results: We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors.
Availability:
http://samtools.sourceforge.net
Contact:
hengli@broadinstitute.org
BFC is a free, fast and easy-to-use sequencing error corrector designed for Illumina short reads. It uses a non-greedy algorithm but still maintains a speed comparable to implementations based on ...greedy methods. In evaluations on real data, BFC appears to correct more errors with fewer overcorrections in comparison to existing tools. It particularly does well in suppressing systematic sequencing errors, which helps to improve the base accuracy of de novo assemblies.
https://github.com/lh3/bfc
hengli@broadinstitute.org
Supplementary data are available at Bioinformatics online.
Tabix is the first generic tool that indexes position sorted files in TAB-delimited formats such as GFF, BED, PSL, SAM and SQL export, and quickly retrieves features overlapping specified regions. ...Tabix features include few seek function calls per query, data compression with gzip compatibility and direct FTP/HTTP access. Tabix is implemented as a free command-line tool as well as a library in C, Java, Perl and Python. It is particularly useful for manually examining local genomic features on the command line and enables genome viewers to support huge data files and remote custom tracks over networks.
http://samtools.sourceforge.net.
I propose a new application of profile Hidden Markov Models in the area of SNP discovery from resequencing data, to greatly reduce false SNP calls caused by misalignments around insertions and ...deletions (indels). The central concept is per-Base Alignment Quality, which accurately measures the probability of a read base being wrongly aligned. The effectiveness of BAQ has been positively confirmed on large datasets by the 1000 Genomes Project analysis subgroup.
http://samtools.sourceforge.net
hengli@broadinstitute.org.
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.
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.
BWA-MEM alignment and raw variant calls are available at http://bit.ly/1g8XqRt scripts and miscellaneous data at https://github.com/lh3/varcmp.
hengli@broadinstitute.org
Supplementary data are available at Bioinformatics online.
FermiKit is a variant calling pipeline for Illumina whole-genome germline data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short ...insertions/deletions and structural variations. FermiKit takes about one day to assemble 30-fold human whole-genome data on a modern 16-core server with 85 GB RAM at the peak, and calls variants in half an hour to an accuracy comparable to the current practice. FermiKit assembly is a reduced representation of raw data while retaining most of the original information.
https://github.com/lh3/fermikit
hengli@broadinstitute.org.
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