:: DESCRIPTION
The program ‘sff2fastq‘ extracts read information from a SFF file,produced by the 454 genome sequencer, and outputs the sequences and quality scores in a FASTQ format.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SPRING is a compression tool for Fastq files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chandak S, Tatwawadi K, Ochoa I, Hernaez M, Weissman T.
SPRING: a next-generation compressor for FASTQ data.
Bioinformatics. 2019 Aug 1;35(15):2674-2676. doi: 10.1093/bioinformatics/bty1015. PMID: 30535063; PMCID: PMC6662292.
:: DESCRIPTION
fqCleanER is a command line tool to ease the different standard preprocessing steps of short high-throughput sequencing (HTS) reads.
::DEVELOPER
Alexis Criscuolo (alexis.criscuolo@pasteur.fr)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
fq2dna is a command line tool to ease the de novo assembly of archaea, bacteria or virus genomes from raw high-throughput sequencing (HTS) paired-end (PE) reads.
::DEVELOPER
Alexis Criscuolo (alexis.criscuolo@pasteur.fr)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
fastq Merger will merge fastqs with the GSL naming convention by their library IDs.
::DEVELOPER
The HudsonAlpha Genomic Services Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
:: DESCRIPTION
FastqCLS is a robust FASTQ-specific compressor for recent generation data via score-based reordering.
:: DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lee D, Song G.
FastqCLS: a FASTQ Compressor for Long-read Sequencing via read reordering using a novel scoring model.
Bioinformatics. 2021 Oct 8:btab696. doi: 10.1093/bioinformatics/btab696. Epub ahead of print. PMID: 34623374.
:: DESCRIPTION
fastqz is a compressor for the most common (Sanger format) FASTQ files produced by DNA sequencing machines. It may be used with a reference genome for better compression.
Fqzcomp is a basic fastq compressor, designed primarily for high performance.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bonfield JK, Mahoney MV (2013)
Compression of FASTQ and SAM Format Sequencing Data.
PLoS ONE 8(3): e59190. doi:10.1371/journal.pone.0059190
:: DESCRIPTION
HPG FastQ – Quality Control, Filtering and Preprocessing of Fastq file
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The program KvarQ performs rapid in silico genotyping for selected loci (e.g. phylogenetic SNPs, drug resistance mutations) in bacterial genome sequences in FastQ format. Mapping to a whole-genome reference sequence or de novo assembly or the short reads is not necessary.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Genomics. 2014 Oct 9;15(1):881. doi: 10.1186/1471-2164-15-881.
KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes.
Steiner A, Stucki D, Coscolla M, Borrell S, Gagneux S
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
