KARMA 0.9 – Aligner for Mapping Shotgun Sequencer FASTQ Read

KARMA 0.9

:: DESCRIPTION

Karma ( K-tuple Alignment with Rapid Matching Algorithm) is an index based high speed aligner for mapping shotgun sequencer FASTQ reads to a reference genome. Karma assembles FASTQ files from Solexa into a set of mapped reads using a genome reference. It does this by first creating a index of the genome reference, then uses portions of the read to index into the reference to find possible matches.

::DEVELOPER

Paul Anderson @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KARMA

:: MORE INFORMATION

SeqMule 1.2.5 – Automated Pipeline for Variant Calling from FASTQ files

SeqMule 1.2.5

:: DESCRIPTION

SeqMule is an automated pipeline to generate variant calls from FASTQ or BAM files, using more than 10 popular alignment and variant calling tools.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Java

:: DOWNLOAD

 SeqMule

:: MORE INFORMATION

Citation

SeqMule: automated pipeline for analysis of human exome/genome sequencing data.
Guo Y, Ding X, Shen Y, Lyon GJ, Wang K.
Sci Rep. 2015 Sep 18;5:14283. doi: 10.1038/srep14283.

TriageTools 0.2.2 – Partitioning and Prioritizing Fastq data

TriageTools 0.2.2

:: DESCRIPTION

TriageTools is a collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects.

::DEVELOPER

TriageTools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 TriageTools

:: MORE INFORMATION

Citation

TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data.
Fimereli D, Detours V, Konopka T.
Nucleic Acids Res. 2013 Apr;41(7):e86. doi: 10.1093/nar/gkt094

BamHash 1.0 – Hash BAM and FASTQ files to verify Data Integrity

BamHash 1.0

:: DESCRIPTION

BamHash is a checksum program for verifying the integrity of sequence data.

::DEVELOPER

Decode Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

   BamHash

:: MORE INFORMATION

Citation:

BamHash: a checksum program for verifying the integrity of sequence data.
óskarsdóttir A, Másson G, Melsted P.
Bioinformatics. 2015 Sep 10. pii: btv539.

simRRLs 1.5 – Simulate fastQ formatted RAD, ddRAD or GBS data on a fixed Species Tree

simRRLs 1.5

:: DESCRIPTION

The script simRRLs.py can be used to simulate RADseq-like sequences on a fixed species tree under a coalescent model. See Example usage page for advanced options, including simulating missing data, indels and different levels of divergence between taxa.

::DEVELOPER

Deren Eaton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 simRRLs

:: MORE INFORMATION

LW-FQZip – Light-weight reference-based compression of FASTQ data

LW-FQZip

:: DESCRIPTION

LW-FQZip is a lossless light-weight reference-based compression tool for FASTQ data.

::DEVELOPER

Zexuan ZHU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LW-FQZip

:: MORE INFORMATION

Citation

Light-weight reference-based compression of FASTQ data.
Zhang Y, Li L, Yang Y, Yang X, He S, Zhu Z.
BMC Bioinformatics. 2015 Jun 9;16(1):188. doi: 10.1186/s12859-015-0628-7.

FASTools 2.0 – Manipulate Files containing DNA sequences in FASTA and FASTQ format

FASTools 2.0

:: DESCRIPTION

FASTools is a collection to command-line tools to manipulate files containing DNA sequences in FASTA and FASTQ format.

::DEVELOPER

University of Florida Genetics Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FASTools

:: MORE INFORMATION

XS – FASTQ Read Simulator

XS

:: DESCRIPTION

XS (eXtra Small)is a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 XS

:: MORE INFORMATION

Citation

BMC Res Notes. 2014 Jan 16;7:40. doi: 10.1186/1756-0500-7-40.
XS: a FASTQ read simulator.
Pratas D1, Pinho AJ, Rodrigues JM.

Sickle 1.33 – Windowed Adaptive Trimming for Fastq files using Quality

Sickle 1.33

:: DESCRIPTION

Sickle is a windowed adaptive trimming tool for FASTQ files using quality. Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3′-end of reads and also determines when the quality is sufficiently high enough to trim the 5′-end of reads. It will also discard reads based upon the length threshold.

::DEVELOPER

Sickle team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • zlib

:: DOWNLOAD

 Sickle

:: MORE INFORMATION

Faster2 0.31 – Extensible Tool for working with FASTA and FASTQ files

Faster2 0.31

:: DESCRIPTION

Faster2 is an extensible C++11 framework and program for efficient access and extraction of DNA sequences from FASTA and FASTQ files. It works with large file collections of raw as well as compressed data, and is based on the set of filters that can be organized into a pipeline. Faster2 performs input data indexing in order to accelerate all supported operations. It can be easily customized and extended with new filters, and its pipeline building sub-system can be incorporated into other tools. Faster2 is not a database system nor a data analytics tool. Its sole purpose is to simplify tedious operations that are part of everyday tasks performed routinely by bioinformaticians and computational biologists, and yet often require writing specialized text-processing scripts. +

::DEVELOPER

Jaroslaw Zola

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Compiler

:: DOWNLOAD

 Faster2

:: MORE INFORMATION