Tag: Sequencing reads

cutadapt v3.4 – Remove Adapter Sequences from DNA Sequencing reads

cutadapt v3.4

:: DESCRIPTION

Cutadapt removes adapter sequences from DNA high-throughput sequencing data. This is usually necessary when the read length of the machine is longer than the molecule that is sequenced, such as in microRNA data.

::DEVELOPER

Marcel Martin @ the Science for Life Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 cutadapt

:: MORE INFORMATION

Citation

Marcel Martin
Cutadapt removes adapter sequences from high-throughput sequencing reads
EMBnet.journal volume 17 pages 10–12

ORCOM 1.0 – Compressor of Sequencing Reads

ORCOM 1.0

:: DESCRIPTION

ORCOM (Overlapping Reads COmpression with Minimizers) is a compressor of sequencing reads. It takes as an input FASTQ files (possibly gzipped) and stores the DNA symbols of each read in a highly-compressed form.

::DEVELOPER

REFRESH Bioinformatics Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 ORCOM

:: MORE INFORMATION

Citation

Disk-based compression of data from genome sequencing.
Grabowski S, Deorowicz S, Roguski Ł.
Bioinformatics. 2014 Dec 22. pii: btu844.

Trowel 0.2.0.4 – Error Correction Module for Illumina Sequencing Reads

Trowel 0.2.0.4

:: DESCRIPTION

Trowel is an error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. This tool is the first tool that uses a quality threshold instead of a coverage cutoff in order to extract trusted k-mers.

::DEVELOPER

Trowel team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

 Trowel

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 29. pii: btu513.
Trowel: a fast and accurate error correction module for Illumina sequencing reads.
Lim EC, Müller J, Hagmann J, Henz SR, Kim ST, Weigel D.

LASER 2.04 – Locating Ancestry using SEquencing Reads

LASER 2.04

:: DESCRIPTION

LASER is a C++ software package that can estimate individual ancestry directly from genome-wide shortgun sequencing reads without calling genotypes.

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 LASER

:: MORE INFORMATION

Citation

Nat Genet. 2014 Apr;46(4):409-15. doi: 10.1038/ng.2924. Epub 2014 Mar 16.
Ancestry estimation and control of population stratification for sequence-based association studies.
Wang C et cl.

SnpStore 1.0 – SNP and Indel Calling in mapped NGS Sequencing Reads

SnpStore 1.0

:: DESCRIPTION

 SnpStore is a program for SNP and indel calling in mapped next-generation sequencing read data. It features a simple threshold-based model for SNP and indel calling, and a MAQ-like Bayesian model for SNP genotype calling.

::DEVELOPER

Anne-Katrin Emde, Tobias Rausch, Stefan Haas, and Knut Reinert

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 SnpStore

:: MORE INFORMATION

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