Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and able 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.
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.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Permits partitioning raw data from high-throughput sequencing (HTS) projects. TriageTools is a toolkit that implements a method, triage by sequence, designed to extract a subset of reads from raw data from HTS based on sequence similarity with a target region. The software also provides other means to manipulate, partition and prioritize the analysis of raw HTS data, such as tools to partition FASTQ data by base quality or to identify (near) duplicate reads.
A suite of software tools for manipulating data common to next-generation sequencing experiments, such as FASTQ, BED and BAM format files. With modules that operate from FASTQ pre-processing through BAM post-processing and RPKM calculations, NGSUtils compliments existing tools and provides unique functionality that helps each step of an NGS data analysis pipeline. NGSUtils covers different aspects of NGS data analysis, including pre-processing, post-processing, filtering, format conversion and final result calculations. NGSUtils provides a stable and modular platform for data management and analysis.
Offers an assortment of tools suited for sequence analysis. Japsa is an open source package that gathers more than 20 tools including a java library and an API. The application provides a wide range of functionalities that allows users to split multiple sequences files, to perform real-time identification of antibiotic resistance gene with Oxford Nanopore sequencing as well as to normalize the branch length of a phylogeny.
Allows users to reformate and filter bioinformatics files. JVARKIT aims to simplify the grammar employed to filter bioinformatic file, for rendering possible to write a loop or a custom function. JVARKIT is a set of more than 100 java-based tools for bioinformatics.
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.
Provides several simple Perl scripts for high throughput genomic and transcriptomic data. NGS-TOOLBOX permits, among others, to calculate the total nucleotide composition and the sequence length distribution. It can remove identical sequences, specified adapter sequences and low-complexity sequences from a dataset. This software can also generate reverse complementary sequences and split large sequence files into smaller parts specified by different parameters.
Assists in processing FASTA files containing DNA and protein sequences. SEDA is an application that allows users to (i) filter sequences based on different criteria (including text patterns), (ii) translate nucleic acid sequences into amino acid sequences, (iii) execute Blast analyses, (iv) remove duplicated sequences, and (v) sort, merge, split or reformat files.
Reads a protein FASTA file and splits it apart into a number of sections. Fasta File Splitter is a console application to break apart a large protein FASTA file into a series of smaller FASTA files, all equally sized. Specify the number of sections using /N. Although the splitting is random, each section will have a nearly identical number of residues. This program are primarily designed to run on Windows machines.
Splits one or more sequences into original source sequences. splitsource processes the "source" features in the feature table. The "source" feature annotated the origin of a sequence region. Synthetic sequences are characterized by having two or more "source" features each describing one of the original sequence fragments.
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