:: DESCRIPTION
LW-FQZip is a lossless light-weight reference-based compression tool for FASTQ data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
BamHash is a checksum program for verifying the integrity of sequence data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
TriageTools is a collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs.However,It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome – manipulating the sequences to produce better mapping results.The FASTX-Toolkit tools perform some of these preprocessing tasks.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Sabre is a tool that will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply compares the provided barcodes with each read and separates the read into its appropriate barcode file, after stripping the barcode from the read (and also stripping the quality values of the barcode bases). If a read does not have a recognized barcode, then it is put into the unknown file.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Sherman is a script to simulate high-throughput sequencing data. It specialises in generating libraries for bisulfite-sequencing (BS-Seq) and introducing various sources of contamination which are commonly found in various Next-Gen Sequencing applications.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
