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SAM/BAM/CRAM file manipulation bioinformatics software tools

Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing…
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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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BEDTools
Desktop

BEDTools

A software suite for the comparison, manipulation and annotation of genomic…

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…

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GATK-Queue
Desktop

GATK-Queue Genome Analysis Toolkit-Queue

A command-line scripting framework for defining multi-stage genomic analysis…

A command-line scripting framework for defining multi-stage genomic analysis pipelines combined with an execution manager that runs those pipelines from end-to-end. Often processing genome data…

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Hadoop-BAM
Desktop

Hadoop-BAM

A Java library for the manipulation of files in common bioinformatics formats…

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.

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BAM-matcher
Desktop

BAM-matcher

A tool that can rapidly determine whether two BAM files represent samples from…

A tool that can rapidly determine whether two BAM files represent samples from the same biological source by comparing their genotypes. BAM-matcher has the following features: first, it is easy to…

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sam2bam
Desktop

sam2bam

Enables users to significantly speed up pre-processing for next-generation…

Enables users to significantly speed up pre-processing for next-generation sequencing (NGS) data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the…

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ATLAS
Desktop

ATLAS Analysis Tools for Low-depth and Ancient Samples

Analyzes ancient samples that properly account for post-mortem damage (PMD).…

Analyzes ancient samples that properly account for post-mortem damage (PMD). ATLAS works directly from raw BAM files and contains all necessary methods to infer patterns of PMD, recalibrate base…

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Sambamba
Desktop

Sambamba

A high performance robust tool and library for working with SAM, BAM and CRAM…

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…

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rbamtools
Desktop

rbamtools

A full spectrum of accessibility to BAM for R users are provided such as…

A full spectrum of accessibility to BAM for R users are provided such as reading, writing, extraction of subsets and plotting of alignment depth where the script syntax closely follows the SAM/BAM…

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NGSUtils
Desktop

NGSUtils

A suite of software tools for manipulating data common to next-generation…

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…

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cljam
Desktop

cljam

An open-source software using Clojure, which is a functional programming…

An open-source software using Clojure, which is a functional programming language that works on the Java Virtual Machine. Cljam can process and analyze SAM/BAM files in parallel and at high speed.…

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SeqLib
Desktop

SeqLib

Provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global…

Provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. SeqLib provides a command-line tool for performing combinations of…

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chopBAI
Desktop

chopBAI

A program that can chop a BAM index (BAI) file into small pieces. The program…

A program that can chop a BAM index (BAI) file into small pieces. The program outputs a list of BAI files each indexing a specified genomic interval. The output files are much smaller in size but…

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VariantBam
Desktop

VariantBam

A C ++ read filtering and profiling tool for use with BAM, CRAM and SAM…

A C ++ read filtering and profiling tool for use with BAM, CRAM and SAM sequencing files. VariantBam provides a flexible framework for extracting sequencing reads or read-pairs that satisfy…

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BamHash
Desktop

BamHash

A checksum based method to ensure that the read pairs in FASTQ files match…

A checksum based method to ensure that the read pairs in FASTQ files match exactly the read pairs stored in BAM files, regardless of the ordering of reads. BamHash can be used to verify the integrity…

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Bio-samtools
Desktop

Bio-samtools

A flexible and easy to use interface that programmers of many levels of…

A flexible and easy to use interface that programmers of many levels of experience can use to access information in the popular and common SAM/BAM format. bio-samtools 2 provides new classes for…

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Scramble
Desktop

Scramble

A conversion tool to read and write SAM, BAM and CRAM formats using a unified…

A conversion tool to read and write SAM, BAM and CRAM formats using a unified Application Programming Interface (API). It also permits the most efficient use of threads when converting between…

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SWEEP
Desktop

SWEEP Sliding Window Extraction of Explicit Polymorphisms

Filters out false positives from a set of single nucleotide polymorphism (SNP)…

Filters out false positives from a set of single nucleotide polymorphism (SNP) calls. SWEEP uses the ubiquitous false-positive SNP calls and transforms them from a weakness to a strength by using…

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deepTools
Desktop
Web

deepTools

A Galaxy based web server for processing and visualizing deeply sequenced data.…

A Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable…

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NGS-Bits
Desktop

NGS-Bits

Permits quality control of Next-Generation-Sequencing (NGS) tumor-normal…

Permits quality control of Next-Generation-Sequencing (NGS) tumor-normal experiments. NGS-Bits is separate into four steps: (1) gather information from raw reads, (2) map reads, (3) extract variant…

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Goleft
Desktop

Goleft

Enables coverage profiling at low computational cost, provides an interactive…

Enables coverage profiling at low computational cost, provides an interactive output that facilitates the detection of coverage anomalies (deletions, duplications, sex chromosome anomalies). Goleft…

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JfxNgs
Desktop

JfxNgs

Can read local files as long as they’ve been indexed with tabix or tribble.…

Can read local files as long as they’ve been indexed with tabix or tribble. JfxNgs is a computational package and a java-based user interface. It can also access the remote files if the hosting…

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BamTools
Desktop

BamTools

A software suite for programmers and end users that facilitates research…

A software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support…

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RACKJ
Desktop

RACKJ Read Analysis & Comparison Kit in Java

A set of Java programs that analyze and compare RNA-seq data made by NGS…

A set of Java programs that analyze and compare RNA-seq data made by NGS technologies. In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing…

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pbbam
Desktop

pbbam

Allows users to obtain PacBio BAM files and their associated indices. pbbam is…

Allows users to obtain PacBio BAM files and their associated indices. pbbam is mainly composed of a core C++ library which permits to create, query and edit files corresponding to the PacBio Bam…

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bamsignals
Desktop

bamsignals

Allows to efficiently obtain count vectors from indexed bam files. bamsignals…

Allows to efficiently obtain count vectors from indexed bam files. bamsignals counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles…

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VarAFT
Desktop

VarAFT Variant Annotation and Filter Tool

Annotates and filtrates variant files. VarAFT allows the comparison of several…

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…

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SAMSVM
Desktop

SAMSVM

Detects and filters the misaligned reads of SAM format. Such filtration can…

Detects and filters the misaligned reads of SAM format. Such filtration can reduce false positives in alignment and the following variant analysis. Cross-validation between two simulated datasets…

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Picard
Desktop

Picard

A set of tools (in Java) for working with next generation sequencing data in…

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

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BioD
Desktop

BioD

Allows users to write bioinformatics applications in D, codebase and helps to…

Allows users to write bioinformatics applications in D, codebase and helps to handle common biological data formats.

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bam‐readcount
Desktop

bam‐readcount

Generates metrics at single nucleotide positions. bam‐readcount is a pipeline…

Generates metrics at single nucleotide positions. bam‐readcount is a pipeline able to report readcounts for each base at each position requested. It also reports the average base quality of these…

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Pysam
Desktop

Pysam

Allows to read and manipulate SAM, BAM, VCF, and BCF files. Pysam focuses on…

Allows to read and manipulate SAM, BAM, VCF, and BCF files. Pysam focuses on SAM and BAM format because they permit to store efficiently large numbers of alignments.

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Parabam
Desktop

Parabam

Allows user to make maximum usage of the processing power available to their…

Allows user to make maximum usage of the processing power available to their machines. Parabam is a python package that allows user to inspect large BAM files in a timely manner whilst making the…

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aligncopy
Desktop

aligncopy

Reads and writes alignments. aligncopy can read a set of aligned sequences and…

Reads and writes alignments. aligncopy can read a set of aligned sequences and reports the alignment using any of the standard EMBOSS alignment formats that can report on the size of the input…

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NovoSort
Desktop

NovoSort

Uses to designe multi-thread sort/merge tools for BAM files. NovoSort reduces…

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…

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bam2fastq
Desktop

bam2fastq PairEnd Bam to Fastq

A simple script for converting pair-end bam files to fastq files. Unlike other…

A simple script for converting pair-end bam files to fastq files. Unlike other bam2fastq scripts this script can handle discordant pairs(pairs mapped to different chromosomes) without sorting the…

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