Search Results for "sam" - Page 3
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Showing 120 open source projects for "sam"
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SeqPig
Use Apache Pig to process your large sequencing datasets!
...It provides import and export functions for file formats commonly used for sequencing data, as well as a collection of Pig user-defined-functions (UDF’s) to help process aligned and unaligned sequence data. Currently SeqPig supports BAM/SAM, FastQ and Qseq input and output. For more information see the manual at http://seqpig.sourceforge.net/ -
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Pathoscope
Predicts strains of genomes in Nextgen seq alignment file (sam/bl8)
This page is here for archival purpose. Please visit github for the latest version of the software: https://github.com/pathoscope PathoScope takes next-generation sequencing reads from a mixture sample and predicts which genomes are present. We use a Bayesian framework combined with an initial reference-based alignment to assign reads to the correct genome of origin. Pathoscope 2.0: Wiki: http://sourceforge.net/p/pathoscope/wiki/Home/... -
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A fork of BOSSA
This is a fork of the BOSSA project by ShumaTech.
BOSSA is a flash programming utility for Atmel's SAM family of flash-based ARM microcontrollers, developed by ShumaTech. The motivation behind BOSSA is to create a simple, easy-to-use, open source utility to replace Atmel's SAM-BA software. This project is a fork, created to temporarily host new modifications to BOSSA until they can be incorporated into the main BOSSA codebase. -
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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). -
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bio-cargo
CARGO - Compressed ARchival for GenOmics
CARGO is a high-level framework that can semi-automatically generate software systems optimized for the compressed storage of arbitrary types of large genomic data collections. Straightforward applications of CARGO methods to compress FASTQ and SAM format archives require only a few lines of code, produce solutions that match and sometimes outperform specialized format-tailored compressors, and scale well to multi-TB datasets. -
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sameflash
Serial flash tool for Atmel M7 core
This tool written in Java uploads HEX files into microcontroller flash and runs it using SAM-BA protocol, as original Atmel tool fails with modern M7 core chips. SAME70 is now supported. Current version does not program GPNVM bit, so after reset program will not start again - just add few lines of code to do that. -
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Sita Access Manager
Sita Access Manager (SAM) is php based Login System.
Sita Access Manager (SAM) is php based and secure login system. -
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iMSAT represents a full update of the vcf2MSAT program. This command line python program allows for a user to use the polymorphism data generated using SAM- and BAM-tools and a .fasta alignment file to search for polymorphic microsatellite markers (MSATs or STRs). By identifying polymorphic makers, rather than simple repeat regions as previous programs have done, iMSAT greatly increases the speed at which polymorphic MSATs that can be identified -- saving researchers precious time and money. ...
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sam_comp
Compression for SAM/BAM file format
This is a simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format. -
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SAMSVM
A tool for misalignment filtration on SAM-format sequences with SVM
Applying the LIBSVM, a package of support vector machine, SAMSVM was developed to correctly detect and filter the misaligned reads of SAM format. Such filtration can reduce false positives in alignment and the following variant analysis. -
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Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. ...
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SuRankCo
Supervised Ranking of Contigs in de novo Assemblies
...Renard (http://www.biomedcentral.com/1471-2105/16/240/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using SuRankCo. Update Jun2015: * Minor changes to enable BAM support. Update Feb2014: * Added support for FASTA/SAM assemblies in addition to ACE/FASTQ(QUAL). NOTE: features of FASTA/SAM assemblies do not include BaseCount, BaseSeqmentCount and ContigQualities yet. -
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Transcriptome assembly ORA
Reference-based transcriptome reconstruction software
...It performs reconstruction starting from short reads obtained from RNA-seq. It is best suited to manage the transcriptomes of lower eukaryotes with a low number of introns per gene and it can be used also for procariotes. It needs a SAM file with the reads aligned on the reference genome and (optional) a gff file with the position of genes on the reference genome. It provides in output the positions of the transcripts identified, the transcripts names based on the genes present on the gff file anf the size of UTR regions. -
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jChIP
Graphical environment for exploratory ChIPSeq data analysis
...It was created to build binding profiles between proteins and loci in the genome. In addition it computes statistics of the number of loci/positions containing specified amount of tags. jChIP is able to load data in several common formats (SAM, BAM, WIG, BED, Bowtie) and download loci definitions directly from the Ensembl database. http://www.biomedcentral.com/1756-0500/7/676 -
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Snort/Snort Sam
Snort/Snortsam by Tran Phuong Binh
Đồ án xây dựng hệ thống cảnh báo và ngăn chặn xâm nhập Trần Phương Bình Lớp C15QM15 MSV: 13204272 HUTECH -
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MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in... -
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MIF85Tracker
chiptune music tracker for Philips SAA-1099
Multiplatform GNU/GPL chiptune music tracker for Philips SAA-1099 soundchip with 6 channels, which was used in Sam Coupé micro-computer and also in sound interface MIF 85 for the Tesla PMD 85 (an 8-bit personal micro-computer produced in eighties of twentieth century in former Czechoslovakia). This is a very first music tracker for this soundchip on PC platform! -
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pyz80 is a z80 cross-assembler written entirely in Python. It accepts text files with the syntax of the Sam Coupe's popular COMET assembler, and outputs a disk image suitable for loading in SimCoupe or transferring to floppy disk for use with a real Sam.
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unixadmin
unixadmin is a system administration tool for Linux and OS X
unixadmin ============ unixadmin (Previously known as smc/syspert) Is a system administration tool which supports all versions of UNIX and Debian based versions and Red Hat versions of Linux, which supports major features such as user administration, disk administration and system administration This program sets to replace smit in IBM AIX and sam in HP-UX This program is the Linux equivlient of smit and SAM in AIX and HP-UX -
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mirUtils
miRNA alignment quantitation based on miRBase annotations
mirUtils provides quantitation of aligned microRNA sequences based on miRBase annotations. Starting from a miRBase-aligned BAM/SAM file, mirUtils reports counts and quality metrics for several taxonomy levels, including miRNA precursor hairpins, hairpin groups and families, mature miRNA loci, mature sequences, and genomic clusters, as well as per-hairpin-position alignment start and base coverage details. -
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picard
A set of tools for working with high-throughput sequencing data
A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team -
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Raspbmc kernel + usbtv support
A raspbmc kernel with support for the Fuschicai Easycap stick
A rebuilt raspbmc kernel with support for the Fushicai Easycap usb grabber (ID 1b71:3002). All credit goes to Sam Nazarko for his brilliant work. Sam, if you can see this, I would appreciate it if you included this module into the next release of Raspbmc :) Please refer to the wiki for installation instructions. All credit goes to Sam Nazarko for the brilliant raspbmc, and all the brilliant people who work on the raspbian and debian kernels - you guys rock! ... -
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Bycom
Bycom can do methylcytosine calling (5mC calling) from BS-seq.
Bycom can do methylcytosine calling from BS-seq (WGBS and RRBS), and either unmapped reads (FASTQ) or mapped reads (SAM/BAM) could be permitted for the input data. Certain SNPs (C>A/G) can also be selected in the output. 1. There's no softwares or methods identify methylcytosines considering the cell heterozygosis caused by multicellular sequencing. Bycom introduced it along with the sequencing errors and unconverson rate based on the Bayesian model. 2.
