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PHRAP

Phrap

Phrap is a widely used program for DNA sequence assembly. It is part of the Phred-Phrap-Consed package. Phrap was originally developed by Prof. Phil Green

Phrap

Phred quality score

Measurement in DNA sequencing

quality scores were primarily used by the sequence assembly program Phrap. Phrap was routinely used in some of the largest sequencing projects in the

Phred quality score

Phred_quality_score

Consed

sequence assemblies. Originally developed for sequence assemblies created with phrap, recent versions also support other sequence assembly programs like Newbler

Consed

Phred (software)

together with another software program called Phrap, which is a program for DNA sequence assembly. Phrap was routinely used in some of the largest sequencing

Phred (software)

Phred_(software)

De novo sequence assemblers

Software in bioinformatics

coverage, and substitution error rate. Software compared: ABySS, Phusion2, phrap, Velvet, SOAPdenovo, PRICE, ALLPATHS-LG N50 analysis: assemblies by the

De novo sequence assemblers

De_novo_sequence_assemblers

ACE (genomic file format)

assemblies. ACE files are generated by various assembly programs, including Phrap, CAP3, Newbler, Arachne, AMOS (more specifically Minimo) and Tigr Assembler

ACE (genomic file format)

ACE_(genomic_file_format)

DNA sequencing

Process of determining the nucleic acid sequence

sequence data which is done by programs and algorithms such as Phred and Phrap. Other challenges have to deal with repetitive sequences that often prevent

DNA sequencing

DNA_sequencing

MacVector

MacVector has a contig assembly plugin called Assembler that uses phred, phrap, Bowtie, SPAdes, Flye, Velvet and cross match. From September 2024 the functionality

MacVector

Staden Package

DNA sequence assembly software

Free and open-source software portal Genome Compiler Phred base calling Phrap Consed CodonCode Aligner MacVector UGENE Vector NTI Bonfield JK, Whitwham

Staden Package

Staden_Package

Metagenomics

Study of genes found in the environment

in order to improve the accuracy of assemblies. Some programs, such as Phrap or Celera Assembler, were designed to be used to assemble single genomes

Metagenomics

List of sequence alignment software

al. 1994 Free, LGPL CodonCode Aligner Multi-alignment; Muscle, Clustal & Phrap support Nucleotides Local or global P. Richterich et al. 2003 (latest version

List of sequence alignment software

List_of_sequence_alignment_software

CodonCode Aligner

DNA sequence software

phylogenetic trees, difference tables, trace sharpening, and support for Phred, Phrap, ClustalW, and MUSCLE. The first beta version of CodonCode Aligner was released

CodonCode Aligner

CodonCode_Aligner