Search Results for "assembly source code" - Page 2
Sort By:
Showing 93 open source projects for "assembly source code"
View related business solutions-
Our Free Plans just got better! | Auth0You asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your security. Auth0 now, thank yourself later.
-
$300 Free Credits for Your Google Cloud ProjectsLaunch your next project with $300 in free Google Cloud credits—no strings attached. Test, build, and deploy without risk. Use your credits across the entire Google Cloud platform to find what works best for your needs. After your credits are used, continue with always-free tier services. Only pay when you're ready to scale. Sign up in minutes and start exploring.
-
1
CSBB-v3.0
CSBB - Computational Suite for Bioinformaticians and Biologists
CSBB is a command line-based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java, python and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux,... -
2
owfs and owhttpd
Project moved to https://github.com/owfs/owfs/
Please note that OWFS source code, and all Issue/Tickets/merge requests have now been moved to https://github.com/owfs/owfs/. Developer mailing lists will still be kept at Sourceforge. ---- OWFS -- 1-Wire file system. Use the Dallas 1-Wire and iButton chips with standard filesystem commands. Create temperature loggers. Monitor everything. OWHTTPD -- same system, only used as a light weight web server. -
3
CSBB-v2.0
Computational Suite for Bioinformaticians and Biologists
CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX and... -
4
ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
...https://hpc.nih.gov/apps/ViralFusionSeq/ ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. VFS combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. Source code with user manual and installation guide of VFS is available at sourceforge's "Files" section. Citation: http://www.ncbi.nlm.nih.gov/pubmed/ -
Go from Code to Production URL in SecondsSkip the Kubernetes configs. Cloud Run handles HTTPS, scaling, and infrastructure automatically. Two million requests free per month.
-
5
XASTIR
Multiplatform Ham Radio APRS and Mapping Program
NOTE: Code commits are FROZEN on SourceForge: New code is now at <http://github.com/Xastir/Xastir>. Real-time tracking & messaging of stations via radio/internet APRS data streams, w/125 map formats supported. Linux/FreeBSD/Solaris/MacOSX/Windows in any of 7 languages. Can also be used for mobile mapping w/GPS. MAILING LISTS ARE AT: PROJECT->WEB SITE. -
6
RGAAT
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format). -
7
iCAS - An Illumina Clone Assembly System
An Illumina clone assembly system using SOAPdenovo and ABySS
Clone-by-clone sequencing, as a means of achieving high quality assemblies for large and complex genomes, continues to be of great relevance in the era of high throughput sequencing. However, assemblies obtained using current whole genome assemblers are often fragmented and sometimes have issues of genome completeness owing to different data characteristics introduced by multiplexed sequencing. With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting... -
8
PLP
Powerfull pre-processor
Powerful Verilog Preprocessor. PLP stands for Perl Pre-processor. Perl is used as "control language" that is embedded in the Verilog code (or any other code) to generate code on the fly. It is used commonly as a Verilog pre-processor but can be used with any target/output language (C, C++, Java, VHDL, plain text etc) -
9
gladTeX
GladTeX -- embed LaTeX-quality images in HTML
GladTeX is a preprocessor that enables the use of LaTeX maths within HTML code. The maths, embedded in <eq>..</eq> tags, as if within $$..$$ in LaTeX, is fed through latex and replaced by images. Additionally, alt-tags are auto-generated which display the LaTeX-equations when the HTML is viewed e.g. with a text mode browser or by someone with vision loss. The project home has moved, please visit https://humenda.github.io/GladTeX -
Custom VMs From 1 to 96 vCPUs With 99.95% UptimeLive migration and automatic failover keep workloads online through maintenance. One free e2-micro VM every month.
-
10
Cadence 614 Installer
Cadence 614 installing scripts with source files
this code include automation for installing Cadence614 with Calibre2011 all you need to do is to install Centos 6.5 32bit on your machine http://archive.kernel.org/centos-vault/6.5/isos/i386/CentOS-6.5-i386-LiveCD.iso and the scripts will do the rest -
11
SPA
SPA: a short peptide assembler for metagenomic data
...Craig Venter Institute, San Diego, CA {yyang,czhong,syooseph}@jcvi.org * Corresponding author SPA is available in binary on 64 bit Linux OS. SFA-SPA is available in binary and source for 64 bit Linux OS. -
12
Automalator
State Dependency deconstructor and mapper for C source code.
Flowcharts not telling you what you want to know about some C source code? Try a State Dependency map! Every C source file is an implemention of a state machine. Implicit in the definition of a state machine is a network of dependencies between the states. The Automalator * deconstructs the C code into the core state machine * collates the transactions into the dependency net * generates a diagram-format file with the states and dependencies as the nodes and edges. ... -
13
Firmware for Cypress' EZ-USB (AN2131) device that lets you use keyboards, mice etc. as USB compliant Human Interface Devices.
-
14
Shoal
A lot of fish in a shoal, in a gigantic scientific ocean.
Ours organization website GCModeller.org is coming online soon! Shoal Shell is the sub project for the "genome-in-code"(http://code.google.com/p/genome-in-code/) virtual cell modelling project of the bacteria Xcc 8004. Shoal Shell aim at provide the modelling tool and the debugging tool for the GCModeller virtual cell modelling, And from the extendible library package, shoal shell can manage to accomplish the entire modelling job for any other bacteria species. Shoal Shell Project... -
15
AMOS
AMOS is a collection of tools for genome assembly
AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation. -
16
The Khepera III Toolbox is a collection of scripts, programs and code modules for the Khepera III robot. It allows for easy access to all sensors and actuators of the robot and provides a lot of standard programs.
-
17
VIGOR3
Annotation of Viral Genomes
VIGOR is a tool for annotating coding genes in viral genomes. It was developed by Jeffrey Hoover and Shiliang Wang for The JCVI Genomic Sequencing Center for Infectious Diseases (GSCID). http://www.biomedcentral.com/content/pdf/1471-2105-11-451.pdf contact: Jeff Hoover 301-540-7858 jefhv@aol.com -
18
CSEA
Correcting Structural Errors After Genome Assembly
CSEA is a suite of programs for correcting structural errors after assembly without reference, improve the quality of genome assembly. The program is specially designed for second-generation sequencing reads. It also can do denovo assembly and correct errors. Contact: jbtangcn@gmail.com -
19
A pipeline to revise a genome sequence of a prokaryotic sample via an iterative backbone remapping and local assembly method.
-
20
primeScaff is intended to automate the sometimes tedious process of manually designing specific primer pairs around gaps of genomic scaffolds and speedup the genome finishing stage of a genome sequencing project. It incorporates de-novo repeat finding using RECON to avoid as much as possible designing primers in repetitive regions and offers the possibility to easily fine-tune the primer design options using primer3. It outputs the repeat, gap and primer annotations in gff2 and gff3 to...
-
21
SpeedyQuant
Quantifies DNA, RNA or protein bands in agarose or acrylamid gels.
...When calculating the relative strength of each band (% of most prominent band) it takes the background noise into account. This leads to accurate and comparable results. Several options can be used to tune the detection process. Here we provide the source code of the program (Perl script) that can be run on any OS with Perl installed (e.g. the freely available Strawberry Perl). A Win-64bit executable is available at: www.foreach-bioinformatics.de -
22
G.R.E.A.T. - Google Earth Reporting Engine and Analysis Tool The Goal of this project is to create a basic IDS interface with Google Earth. Currently generates a KML file of traceroute/whois information suitable for use in Google Earth
-
23
Assembly of mixed genomes
Scripts used to assemble and deconvolute mixed mitochondrial genomes.
Perl scripts used in the paper "Index-free de novo assembly and deconvolution of mixed mitochondrial genomes" by McComish BJ, Hills SFK, Biggs P and Penny D (2010) Genome Biology and Evolution 2:410-424. -
24
Circonspect is a bioinformatic tool to produce contig spectra, useful for the estimating viral diversity in metagenomes. It uses an external assembly program and a bootstrap technique to automate the generation of contig spectra and cross-contig spectra.
-
25
A resource for political accountability; a compilation of statistics and information on Canadian Members of Parliament, and possibly other levels of government. The project includes the website code, as well as the tools used to extract the informati
