Paired-end read elongation software tools | De novo sequencing data analysis
Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome.
Allows users to process biological sequencing data. ea-utils works with pipeline based on Illumina and can run with other FASTQs. It offers several functions such as scanning a sequence file for adapters to determine a set of clipping parameters and perform clipping. It can demultiplex FASTQ files and can check if the reads are in-sync during the demultiplexing.
Produces merged raw Illumina paired-end reads with low false positive rates (FPRs). PEAR combines reads by maximizing the assembly score (AS) of the read overlap via a scoring matrix. It evaluates all possible paired-end read overlaps and does not require the target fragment size as input. This method takes quality scores and sequence matches into account.
Offers a solution for analyzing desktop sequencing data produced by the Roche Junior, Illumina MiSeq or ION PGM™. NextGENe is a program that includes analysis modules for: copy number variation (CNV), alternate splicing of exons and transcript expression levels, single nucleotide polymorphism (SNP)/INDEL and structural variant analysis (resequencing and Amplicon analysis), prediction and rare disease discovery, as well as whole genome alignment or transcriptome.
A comprehensive tool for analyzing next-generation sequencing data. AdapterRemoval is able to pre-process both single and paired-end data. The program locates and removes adapter residues from the reads, it is able to combine paired reads if they overlap, and it can optionally trim low-quality nucleotides. Furthermore, it can look for adapter sequence in both the 5' and 3' ends of the reads. This is a flexible tool that can be tuned to accommodate different experimental settings and sequencing platforms producing FASTQ files. AdapterRemoval is shown to be good at trimming adapters from both single-end and paired-end data.