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GATK / Genome Analysis ToolKit
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Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and ables to support projects of any size. The application compiles an assortment of command line allowing one to analyze of high-throughput sequencing (HTS) data in various formats such as SAM, BAM, CRAM or VCF. The website includes multiple documentation for guiding users.
SAMtools
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Allows users to interact with high-throughput sequencing data. SAMtools permits the manipulation of alignments in the SAM/BAM/CRAM formats: reading, writing, editing, indexing, viewing and converting SAM/BAM/CRAM format. It limits the mapping quality of reads with excessive mismatches and applies base alignment quality to fix alignment errors. This tool can sort and merge alignments, remove polymerase chain reaction (PCR) duplicates or generate per-position information.
BEDTools
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A software suite for the comparison, manipulation and annotation of genomic features in browser extensible data (BED) and general feature format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets.
Sambamba
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A high performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing (NGS) data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces processing time. Sambamba is being adopted at sequencing centers, not only because of its speed, but also because of additional functionality, including coverage analysis and powerful filtering capability.
VarAFT / Variant Annotation and Filter Tool
Annotates and filtrates variant files. VarAFT allows the comparison of several individuals and the collection of relevant information about the variations. It includes a coverage analysis module to easily visualize regions that are poorly covered though tables and dynamic charts. With VarAFT, users can annote variant (VCF) files, combine multiple samples from various individuals, prioritize list of variants by multi-filtering parameters. Additionnaly, users can perform a coverage analysis and quality check from any BAM file.
VCFtools
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Permits users to parse, analyze and manipulate VCF files. VCFtools is a software package for composed of two modules: the first is a general API that allows various operations to be performed on VCF files, including format validation, merging, comparing, intersecting, making complements and basic overall statistics; the second module analyze single-nucleotide polymorphism (SNP) data in VCF format, assisting researchers to estimate allele frequencies, levels of linkage disequilibrium and various quality control (QC) metrics.
Picard
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Assists users in manipulating high-throughput sequencing (HTS) data and formats. Picard is a Java toolkit that provides a set of command line scripts. It comprises Java-based utilities that manipulate SAM files, and a Java API for creating new programs that reads and writes SAM files. Both SAM text format and SAM binary (BAM) format are supported. It also works with next generation sequencing (NGS).
FASTX-Toolkit
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A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information). The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others.
Fragment Merger Tool
Merges long overlapping sequence fragments. Fragment Merger Tool is a genome-agnostic, web-based, assembly software developed using hepatitis B virus (HBV) sequence data. It allows automated assembly of two to twelve long overlapping sequence fragments and enables assembly of sequence data from insertion or deletion mutants and recombinants, as a reference sequence is not used for assembly. The software can be used by researchers without specialist computer skills.
union
Concatenates multiple sequences into a single sequence. union reads in several sequences, concatenates them and writes them out as a single sequence. The input is typically a list file containing references to multiple sequences or subsequences (regions of a sequence). Optionally, feature information will be used. The output can have source features generated which document composite sequences in the EMBL/GenBank feature table. The -findoverlap option checks for overlaps between adjacent joined regions and reports them in the overlap file.
NovoSort
Uses to designe multi-thread sort/merge tools for BAM files. NovoSort reduces run times from multi-threading and by combining sort & merge in one step. It uses a stable sort/merge algorithm that will not change the order of alignments with the same sort key and can optionally create BAM index file. This is a two phase sort merge, the first phase sorts as many reads as possible in memory and then writes segments of sorted records to temporary disk files. The second phase merges the sorted fragments to produce the final sorted file.
FASconCAT
Concatenates different nucleotide, amino acid and structure sequence fragments of same taxa to one super matrix file in format which can be used for phylogenetic purposes. FASconCAT extracts taxon specific associated gene- or structure sequences out of given input files and links them to one string. Missing taxon sequences in single files are replaced either by 'N', 'X' or by 'dots', dependent on their taxon associated data level (nucleotide, amino acid or "dot-bracket" structures).
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