Search Results for "samtools"
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Showing 21 open source projects for "samtools"
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SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools
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TARGT pipeline
Targeted Analysis of sequence Reads for GenoTyping of HLA/MHC genes
...The pipeline consists of a main bash script that calls the different steps of the pipeline and can either be called directly or submitted to a cluster queue system, as well as additional sub-scripts and files, that are required to perform the different steps. The pipeline also requires installed versions of the mapping tool Bowtie2 and samtools. -
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Extract 16S rRNA from genomes
This script extracts 16S rRNA sequences from multifasta files
...This script extracts 16S rRNA sequences from multifasta files present in the folder reported as first argument. It works only in unix system and requires nhmmer and samtools software installed in the system path (if not in system path modify the path at lines 21,72 (for nhmmer),51,100 (for samtools) of the script by adding the path to your nhmmer executable). The HMM files arc.ssu.rnammer.hmm and bac.ssu.rnammer.hmm have to be in the same software were executable file is saved. Inside the folder creates two sub-folders named "bacteria" and "archaea" where you will save your multifasta files (multifasta of bacteria in one and of archaea in the other one). ... -
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fusion-test
Script for fusion detection in DNAseq and RNAseq
...It uses chimerascan, SOAPfuse, MapSplice2, FusionMap, fusioncatcher, TopHat and EricScript. The output files of chimerascan are further annotated by Jinja and Pegasus Fusion. ***Updated*** Note: EricScript uses old version of Samtools. Download the modified program and Samtools-0.1.19 here. An error in the configuration for fusioncathcer is corrected. FusionMap has been deprecated. It is changed to Oshell. The old FusionMap is moved to fusionmap.sh. MapSplice is updated to 2.2.2. -
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YFitter
Fitting Y chromosome haplogroups by maximum likelihood
Yfitter is a program for assigning Y chromosome haplogroups to individuals sequenced at low coverage. It is designed to be used in a samtools/bcftools pipeline. Yfitter also supports haplogrouping using chip genotype data. -
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PPLine
SNP calling, annotation and gene/transcripts expression quantification
...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 of the results -
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Identifies rRNA, contaminants, trims in a standard fashion etc. Maintains read pairs. Built for fire-and-forget high throughput projects (terabytes of data). Uses pbzip2, bowtie2, fastx_toolkit, samtools, fastqc, Trimmomatic (optional)
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SPANDx
Comparative analysis of haploid next-generation genome sequence data
SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data. SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. Annotated, genome-wide SNPs and indels can also be identified if specified, and are output in human readable format. A... -
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BamBam
Tools for genomic analysis
...Tools are provided for calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more. Depends on SAMtools (http://samtools.sourceforge.net/) and BAMtools (https://github.com/pezmaster31/bamtools). Also uses BioPerl, which is included in the download tarball. -
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VarScan
Variant detection in next-generation sequencing data
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB -
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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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BIRAP
Bacterial Intergenic Region Analysis Pipeline
...The tool integrates expression profile derived from RNA-seq and/or proteogenomics, compares it with existing in silico annotation and helps validate annotation, identify novel protein coding regions, putative non-coding RNA as well as help correct er-rors in the existing annotation. The pipeline requires “pileup” output from SAMtools for RNA-seq data and peptide/ePST locus file (GFF) from the Proteogenomic Mapping tool for prote-ogenomics data along with the genome and existing in silico annotation. When information regarding the locus of promot-ers and terminators in the genome (in .coords format) is pro-vided, the pipeline will also help identify non-coding RNA. -
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openSEQ
NGS compute distro proloaded with pipeline analysis software
...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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AFSM_seq
a simple and rapid method for genome-wide SNP and methylation site
...Classified paired-ends using fltfastq2pe.pl. to produce output “R1.trim.pair.fastq” and “R2.trim.pair.fastq”. 4.The filtered sequence reads were aligned to the reference genome using the Bowtie2, allowing a maximum of four mismatches and one gap of up to 3 bp. Using the SAMtools pileup command the variable positions (SNPs) were determined. 5.AFSM_meth_V_1.0.pl are used for analyses of AFSM methylation results were based on comparisons of assembled sequences . perl AFSM_meth_V_1.0.pl -i output.sort.bam -o output.meth.matrix -
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estMOI
estimating Multiplicity Of Infection using short read sequence data
...Short reads are aligned to a reference genome using 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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SOAPindel2
SOAPindel2 focusing on calling indels from the next-generation p
...The files with read-alignments. SOAPindel2 accepts only Indexed BAM formats as input. Users can use the tools/soap2sam.cc to convert SOAP format to SAM format and use samtools convert SAM to indexed BAM. SOAPindel2 can guess the library insert sizes by itself. Sequencing platform:Theoretically, SOAPindel2 is designed for all paired-end sequencing data because it doesn’t consider any qualities for now. So it works for both Ilumina GA data and 454 data, but we’ve only tested it on Ilumina GA data. -
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vcf2MSAT
Find Microsatellites in a ".vcf" report
vcf2MSAT is a python program to identify microsatellite repeat regions based on known polymorphisms identified in a ".vcf" report after using SAMtools to analyze next-generation sequencing files. -
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BCP
NGS analysis tool
BCP is a command-line tool ideated to analyze NGS data, also offering a wrapper for some common NGS software, including Fastx and Samtools. It is oriented mainly towards targeted resequencing experiments, with a set of functions for general purposes. BCP also includes a function for breast cancer risk estimation, based on the Gail model, using both clinical and genome data. -
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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 and returned. Thus, it is easy to use Gaea for developing different customized, scalable analysis pipelines corresponding to the needs of specific research problems in different domains.
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