The presence of duplicates introduced by PCR amplification is a major issue in paired short reads from next-generation sequencing platforms. These duplicates might have a serious impact on research applications, such as scaffolding in whole-genome sequencing and discovering…
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cd-hit-454
Desktop

cd-hit-454

A program to identify artificial duplicates from raw 454 sequencing reads,…

A program to identify artificial duplicates from raw 454 sequencing reads, including exact duplicates and near identical duplicates.

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JATAC
Desktop

JATAC

Filtering duplicate reads from 454 pyrosequencing data.

Filtering duplicate reads from 454 pyrosequencing data.

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FastUniq
Desktop

FastUniq

A fast de novo duplicates removal tool for paired short reads.

A fast de novo duplicates removal tool for paired short reads.

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Fulcrum
Desktop

Fulcrum

Condensing redundant reads from high-throughput sequencing studies.

Condensing redundant reads from high-throughput sequencing studies.

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QUASR
Desktop

QUASR Quality Assessment of Short Read

A lightweight pipeline written to process and analyse next-generation…

A lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms.

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BIGpre
Desktop

BIGpre

A quality assessment package for next-genomics sequencing data. BIGpre contains…

A quality assessment package for next-genomics sequencing data. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read…

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Tally
Desktop

Tally

A package to deduplicate sequence fragments. Tally removes redundancy from…

A package to deduplicate sequence fragments. Tally removes redundancy from sequence files by collapsing identicle reads to a single entry while recording the number of instances of each. It can also…

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Picard
Desktop

Picard

A set of tools (in Java) for working with next generation sequencing data in…

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

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Duplicate…
Desktop

Duplicate reads removal

This tool is specifically well-suited to handle duplicate reads coming from PCR…

This tool is specifically well-suited to handle duplicate reads coming from PCR amplification errors which can have a negative effect because a certain sequence is represented in artificially high…

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RepeatSoaker
Desktop

RepeatSoaker

Removes reads overlapping low-complexity (repeat) regions from aligned…

Removes reads overlapping low-complexity (repeat) regions from aligned sequencing data. RepeatSoaker helps to emphasize the biological signals within the data, reflected by more significant p-values…

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PyroTrimmer
Desktop

PyroTrimmer

Removes the barcodes, linkers, and primers, trims sequence regions with low…

Removes the barcodes, linkers, and primers, trims sequence regions with low quality scores, and filters out low-quality sequence reads. Although these functions have previously been implemented in…

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G-CNV
Desktop

G-CNV GPU-copy number variation

A graphics processing unit (GPU)-based tool for preparing data to detect copy…

A graphics processing unit (GPU)-based tool for preparing data to detect copy number variations (CNVs) with read-depth methods. G-CNV can be used to (i) filter low-quality sequences, (ii) mask…

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ParDRe
Desktop

ParDRe

A de novo parallel tool to remove duplicated and near-duplicated reads through…

A de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of single-end or paired-end sequences from fasta or fastq files. ParDRe uses a novel bitwise approach to…

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ngscmd
Desktop

ngscmd

A C program to manipulate next-generation sequence data files. The ngscmd…

A C program to manipulate next-generation sequence data files. The ngscmd program can work on a single fastQ input file, as well as mate pair files. The fastQ files can be input into the ngscmd…

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DALIGNER
Desktop

DALIGNER

Finds all significant local alignments between reads. DALIGNER can also be used…

Finds all significant local alignments between reads. DALIGNER can also be used as a general read mapper and string to string comparison tool, as a “read” can now be a DNA sequence that is as…

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SAMBLASTER
Desktop

SAMBLASTER

A tool to mark duplicates and extract discordant and split reads from SAM files.

A tool to mark duplicates and extract discordant and split reads from SAM files.

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biobambam
Desktop

biobambam

An API for efficient BAM file reading supporting the efficient collation of…

An API for efficient BAM file reading supporting the efficient collation of alignments by read name without performing a complete resorting of the input file.

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DupRecover
Desktop

DupRecover

A Maximum Likelihood estimator for sampling-induced read duplication in deep…

A Maximum Likelihood estimator for sampling-induced read duplication in deep sequencing experiments.

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