:: DESCRIPTION
AceParser: Parse an Ace file (Phred/Phrap output) into a tab-delimited assembly alignment file. Options to include embedded annotation from multiple sources.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Phred reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.
phrap is a program for assembling shotgun DNA sequence data. Among other features, it allows use of the entire read and not just the trimmed high quality part, it uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats, it constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus, it provides extensive assembly information to assist in trouble-shooting assembly problems, and it handles large datasets.
Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the user to pick primers and templates, suggesting additional sequencing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
:: DESCRIPTION
bcm-ace-plots reads in an Ace format assembly file produced by the Phrap (Green et al.) assembly software. Using special tags in the read names, bcm-ace-plots will plot the template coverage, the template span, the coverage, the BAC coverage, the WGS coverage, quality, and high quality discrepancies.
::DEVELOPER
Human Genome Sequencing Center, Baylor College of Medicine
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Phrap UMD consists of the UMD Trimmer, UMD Overlapper and a modified version of Phrap.It is capable of assembling data downloaded directly from the NCBI Trace Archive. The pipeline runs in 3 stages: first the vector ends of the reads are examined and the vector is found. Then the reads are trimmed for vector and quality. After that the trimmed reads afe fed into the 5-pass UMD Overlapper that finds the overlaps, corrects the base caller errors and performs additional trimming if necessary. After the overlaps are produced, the trimmed and error-corrected reads and overlaps are input into the modified version of Phrap, whichonly puts the reads together if they overlap according to the list of overlaps produced by the UMD Overlapper.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PLoS One. 2008 Mar 19;3(3):e1836.
Improving Phrap-based assembly of the rat using “reliable” overlaps.
Roberts M, Zimin AV, Hayes W, Hunt BR, Ustun C, White JR, Havlak P, Yorke J.
