Cap3 Sequence Assembly Program Windows Apps

Cap3 Sequence Assembly Program Windows Apps 2017
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Suite of tools for assembly, alignment, and analysis of short read next generation sequencing data Unix/Linux, macOS: GPL: BGI: Staden Package: Sequence assembly, editing, and analysis, mainly consisting of gap4, gap5, and spin. Written in C, C, Fortran and Tcl. Linux, macOS, Windows: BSD: Wellcome Trust Sanger Institute, Medical Research Council. Avalanche Workbench is a visual data analysis & DNA sequence data mining tool for biologists. It offers a visual graphic interface through which you can search (eSearch, eLink, eSummary, eFetch) biology databases such as NCBI or get visual access to sequence processing tools/servers. Fasta/FastQ merger. And improvement of sequence assembly programs are required to meet the challenges of the human, mouse, and maize genome projects. We have developed the third generation of the CAP sequence assembly program (Huang 1992). The CAP3 program includes a number of improvements and new features. A capability to clip 58 and 38 low. This mode of assembly uses the global assembly program CAP3, developed by Xiaoqiu Huang. DNA Sequence Assembly under Forward-Reverse Constraints. The CAP3 program can be accessed via the Gap4 interface through the 'Assembly' menu or as a stand alone program.

Bandage is a program for visualising de novo assembly graphs. By displaying connections which are not present in the contigs file, Bandage opens up new possibilities for analysing de novo assemblies.

Features

Load multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA.
Position nodes automatically with an efficient graph layout algorithm.
Zoom, pan and rotate the view using either mouse or keyboard controls.
Reposition and reshape nodes by clicking and dragging with the mouse.
Configure graph scope: view the entire assembly graph or only a region of interest.
Copy node sequences to the clipboard or save them to file.
Colour nodes using built-in colour schemes or user-defined colours.
Label nodes using node number, length, coverage or user-defined labels.
Find nodes quickly in a large graph using node numbers.
Specify the thickness of nodes and allow thickness to reflect the node's read depth.
Define the relationship between the length of a node and the length of its sequence.
Draw graph in single node style: each node and its reverse complements appear as a single object.
Draw graph in double node style: nodes and their reverse complements appear as separate objects with arrow heads to indicate direction.
Highlight and label specific sequences with integrated BLAST search.
Automatically identify nodes contiguous with a node of interest.
Call Bandage from the command line to specify settings, load graphs or generate images.

Uses

Assess and compare the quality of assemblies quickly and visually.
Identify problematic regions of an assembly.
Resolve ambiguities in the graph to improve or complete de novo assemblies.
Determine which other nodes have sequences that are contiguous with a node of interest.
Annotate graph images to illustrate assembly features.
Extract candidate sequences that extend through multiple nodes.

Installation

Bandage works equally well on OS X, Linux and Windows. Users are encouraged to download 64-bit binary executables using the links on the top-right of this page. No installation is necessary – just unzip and run. Windows and Mac binaries come packaged with all necessary libraries. The Linux binary has a couple of dependencies, specified in the zip file. More pre-built binaries are available on the GitHub 'Releases' page.

When first opening Bandage on a Mac, you may receive a warning stating that Bandage 'can't be opened because it is from an unidentified developer.' Right click on the file and select 'Open' to override this warning.

Alternatively, you can clone the source code from GitHub and build Bandage yourself. Instructions are on the GitHub page.

Sample data

Here are a couple of sample graph files you can download and view in Bandage:

An E. coli assembly from Velvet. The reads and more information are available here.
A small mouse transcriptome assembly from Trinity. This data comes with Trinity in the 'sample_data/test_Trinity_Assembly/' folder.

Documentation

Bandage's documentation is on the Bandage GitHub wiki.

Cite

Cap3 Sequence Assembly Program Windows Apps 2017

If you use Bandage in your research, please cite the following publication:

Phred

The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.

The quality value is a log-transformed error probability, specifically

Q = -10 log₁₀( P_e )

where Q and P_e are respectively the quality value and error probability of a particular base call.

The phred quality values have been thoroughly tested for both accuracy and power to discriminate between correct and incorrect base-calls.

Phred can use the quality values to perform sequence trimming.

Phred works well with trace files from the following manufacturers' sequencing machines: Amersham Biosciences, Applied Biosystems, Beckman Instruments, and LI-COR Life Sciences. See the phred documentation for specific compatibility information.

Phred runs on most computers and operating systems including Apple Mac OS X, *BSD, Hewlett-Packard HP-UX, HP-Compaq Tru64, IBM AIX, Linux, Microsoft Windows, Silicon Graphics IRIX, and SUN Solaris.

We distribute phred as 'C' source code: in order to run it you need a 'C' compiler.

See the phred documentation for additional information.

References:

Ewing B, Green P: Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Research 8:186-194 (1998).
Ewing B, Hillier L, Wendl M, Green P: Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research 8:175-185 (1998).

Cap3 sequence assembly program windows apps download

Phrap/Cross_match/Swat

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. See the phrap/cross_match/swat documentation and phrap documentation for additional information.