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…
Desktop app
G T A T C G C T A cd-hit-454 cd-hit-454

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.

Desktop app
G T A T C G C T A Quality Assessment of… Quality Assessment of Short Read

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.

Desktop app
G T A T C G C T A FastUniq FastUniq

FastUniq

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

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

Desktop app
G T A T C G C T A JATAC JATAC

JATAC

Filtering duplicate reads from 454 pyrosequencing data.

Filtering duplicate reads from 454 pyrosequencing data.

Desktop app
G T A T C G C T A Fulcrum Fulcrum

Fulcrum

Condensing redundant reads from high-throughput sequencing studies.

Condensing redundant reads from high-throughput sequencing studies.

Desktop app
G T A T C G C T A BIGpre BIGpre

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…

Desktop app
G T A T C G C T A Tally Tally

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…

Desktop app
G T A T C G C T A Picard Picard

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.

Desktop app
G T A T C G C T A Duplicate reads… Duplicate reads removal

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…

Desktop app
G T A T C G C T A RepeatSoaker RepeatSoaker

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…

Desktop app
G T A T C G C T A PyroTrimmer PyroTrimmer

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…

Desktop app
G T A T C G C T A GPU-copy number… GPU-copy number variation

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…

Desktop app
G T A T C G C T A ParDRe ParDRe

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…

Desktop app
G T A T C G C T A ngscmd ngscmd

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…

Desktop app
G T A T C G C T A DALIGNER DALIGNER

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…

Desktop app
G T A T C G C T A SAMBLASTER SAMBLASTER

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.

Desktop app
G T A T C G C T A biobambam biobambam

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.

Desktop app
G T A T C G C T A DupRecover DupRecover

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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