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.
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.
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).
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.
Enables users to process sequences in FASTA and FASTQ formats. Seqtk parses both FASTA and FASTQ files which can also be optionally compressed by gzip. This application also permits to convert ILLUMINA files to FASTA and to mask bases with low quality. In addition, it includes an option to extract sequences with a specific name or in specified regions.
Provides several programs allowing users to perform both common and uncommon tasks with FASTQ files. fastq-tools is a toolkit that provides tools for (1) finding reads matching a regular-expression, (2) counting k-mer occurances, (3) performing local alignment against every FASTQ sequence, (4) sample reads with or without replacement, (5) sorting FASTQ files and (6) filtering reads with identical sequences.
Resamples biomolecular sequence data. SERES is composed of a merging of non- and semi-parametric approaches with the aim of assisting users in support assessment. It can be applied to both aligned and unaligned sequences. The application gathers a bootstrap method to a Heads-or-Tails (HoT) technique that allows users to run both empirical or simulation studies on SERES local tree annotation.