Search Results for "bowtie"
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Showing 18 open source projects for "bowtie"
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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GenSeed-HMM
Progressive assembly tool using DNA, protein or profile HMMs as seeds.
... The first seed is provided by the user, and can be a piece of DNA or protein sequence, or an HMM profile, for increased sensitivity. This program depends on BLAST+ or hmmsearch and a number of third-party support tools (EMBOSS' transeq and splitter, bowtie, 454's sfffile and sffinfo). Which tools will be mandatory depends on the kind of seed and assembler used. Assemblers currently supported include CAP3, Newbler, SOAPdenovo, Velvet, and Abyss. -
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Bowtie
Create a dashboard with python!
Bowtie is a library for writing dashboards in Python. No need to know web frameworks or JavaScript, focus on building functionality in Python. Interactively explore your data in new ways! Deploy and share with others! Bowtie uses Yarn to manage node packages. If you installed Bowtie through conda, Yarn was also installed as a dependency. Yarn can be installed through conda. An early integration with Jupyter has been prototyped. I encourage you to try it out and share feedback. I hope... -
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hppRNA
A Snakemake-based handy parameter-free pipeline for RNA-Seq analysis
... six core-workflows such as (1) Tophat - Cufflink - Cuffdiff; (2) Subread - featureCounts - DESeq2; (3) STAR - RSEM - EBSeq; (4) Bowtie - eXpress - edgeR; (5) kallisto - sleuth; (6) HISAT - StringTie - Ballgown. Please cite the following paper when using this package: Dapeng Wang. hppRNA—a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples. Briefings in Bioinformatics, Volume 19, Issue 4, 20 July 2018, Pages 622–626. -
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PPLine
SNP calling, annotation and gene/transcripts expression quantification
PPLine is a Python-based suite aimed to process raw RNA-seq or Exome-seq data. PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration... -
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MethyMer
Design of specific primer combinations for bisulfite sequencing
MethyMer is a Python-based tool aimed at selecting specific primers for amplification of complete CpG islands. These regions are difficult in terms of selection appropriate primers because of their low-complexity, polyN-, CG-richness, etc. MethyMer have a flexible scoring system capable of selecting primers in problematic regions (e.g. SpG islands) and includes specificity test (based on bowtie alignment against bisulfite-treated genome). It also incorporates TCGA CpG methylation... -
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Faligner
Faligner: a Local Sequence Alignment Ubuntu Package
A package based on 3 local alignment tools i.e., Bowtie, Bowtie2 and BWA. Package covers single-end, paired-end alignments. Moreover, the package also demonstrates overlap alignment and colorspace alignment features. The package also includes graphical user interface to make it interactive. -
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Protospacer Workbench
CRISPR/Cas9 guide-RNA design
Protospacer Workbench helps to design, analyze, and share CRISPR target-sites for any organism or set of FASTA formatted sequences. Design of guide-RNAs for the CRISPR/Cas genome editing system is intuitively easy, but computationally difficult. The main difficulty arises from the need to identify potential off-targets that may be quite different from the intended target. Current online tools for guide-RNA design provide a user friendly interface to sequence mapping software such as Bowtie... -
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MutAid
MutAid: Sanger and NGS based pipeline for mutation screening.
... mapping, variant calling, variant annotation and co-analyze Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as deletions and insertions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms (Sanger, Illumina, 454 and Ion Torrent) and five read mappers including BWA,TMAP, Bowtie,Bowtie2 and GSNAP and four variant... -
Picsart Enterprise Background Removal API for Stunning eCommerce VisualsWith our Remove Background API tool, you can access the transformative capabilities of automation , which will allow you to turn any photo asset into compelling product imagery. With elevated visuals quality on your digital platforms, you can captivate your audience, and therefore achieve higher engagement and sales.
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ncPRO-seq
Non-Coding RNA PROfiling from sRNA-seq
ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, piRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. ############# Docker version : download and run Dockerfile (go in... -
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jChIP
Graphical environment for exploratory ChIPSeq data analysis
jChIP is a GUI-based Java application for ChIP-Seq 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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openSEQ
NGS compute distro proloaded with pipeline analysis software
.... The first homepage tab links to our pipeline constructer. The second homepage tab links to a xterm session on the client. Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk -
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InMethyl
Design of target-specific primers for bis. sequencing of CpG-islands
InMethyl is a Python-based application for the design of target-specific primer combinations for PCR amplification and bisulfite sequencing of complete CpG-islands. InMethyl uses bowtie high-throughoutput aligner to identify potential mis-priming sites in the bisulfite treated or intact genome and then – undesirable potential PCR products. InMethyl provides a balance between various characteristics that allows to pick up primers in hard-to-study genomic regions. This balance is based... -
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Software quality assurance is essential in genomic medicine. Nonetheless there is currently no systematic evaluation of existing computational tools used for whole genome or whole exome sequencing data analysis. We developed a Metamorphic Testing tool that tests three widely used short-read alignment programs (BWA, Bowtie and Bowtie2) in order to systematically evaluate their performance.
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estMOI
estimating Multiplicity Of Infection using short read sequence data
... BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file. 2. Single Nucleotide Polymorphysms (SNPs) are then identified using SAMTools in the VCF format. 3. The reference FASTA file is expected to be indexed using 'samtools faidx' to generate a *.fai file. estMOI generates files containing MOI estimates for each SNP combinations (file with name *.LOG) and a summary for all chromosomes (file with name *.txt). Contact: samuel.assefa @ lshtm.ac.uk -
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Tuque
Tools for mapping RNA-Seq reads to eukaryotic genomes
Tuque includes 4 programs: tuqueIndex to prepare Bowtie indexes that include spliced sequences tuqueMap to map reads using the prepared indices tuqueSplice to find splice junctions from the reads tuqueCount to count the reads mapping within annotated sequence intervals -
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BowTIE (Brass Technique Instruction Environment) is an application designed to help trumpet, horn, euphonium, and tuba players learn fingering technique. BowTIE provides excellent support for trumpet and horn players who are learning to transpose.
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Gaea
Gaea is designed for re-sequencing tasks.
Serving as a flexible cloud-based framework, Gaea includes the majority of currently popular algorithms for sequence alignment (SOAP2, Bowtie, and BWA) and biomarker discovery (SOAPsnp, SAMtools, and Dindel). It surpasses the performance of currently available alignment software by aggregating their advanced functionalities into a unified cloud-based solution. Due to the internal Hadoop infrastructure, intermediated results from different software algorithms can be efficiently organized...
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