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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.
Source text:
(Magoč and Salzberg, 2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics.

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BBMap
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Uses as a splice-aware aligner for short and long reads. BBMap is shown to be a fast and accurate aligner, capable of correctly handling an overall wider variety of references, reads, and mutations than others. It has particularly outstanding performance with deletions, especially long ones, that other aligners cannot handle at all. It can output many different statistics files, such as an empirical read quality histogram, insert-size distribution, and genome coverage, with or without generating a sam file.
ELOPER
Proceeds by simultaneously considering both ends of paired reads generating elongated reads. ELOPER is a pre-processing tool for pair-end sequences that produces a better read library for assembly programs. It theoretically doubles read-lengths while halving the number of reads. This method exploits the notion that the paired-end information essentially doubles the read length, permitting the detection of up to double the original overlap while maintaining the minimum required sequence overlap. ELOPER thus provides a valuable pre-processing for improved de novo assemblies of short paired-end libraries.
AdapterRemoval
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.
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