Search Results for "fastq" - Page 2
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Showing 46 open source projects for "fastq"
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AFSM_seq
a simple and rapid method for genome-wide SNP and methylation site
Reference based analysis 1.Filter the raw reads obtained from Illumina Raw Data (paired-ends)according to your desired stringency, to produce a set of high-quality (HQ) sequences in fastq format. 2.Lignment reads (HQ, Fastq format) against Barcode file (Fasta format) using scanAP program. 3.Trim barcodes and filter paired-ends using trim_seq.pl. Classified paired-ends using fltfastq2pe.pl. to produce output “R1.trim.pair.fastq” and “R2.trim.pair.fastq”. 4.The filtered sequence reads were aligned to the reference genome using the Bowtie2, allowing a maximum of four mismatches and one gap of up to 3 bp. ... -
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NGSimple
NGS - Next-Generation Sequencing sIMulation PipeLinE
...It's recommended to start with a short reference (~5M bases), in case that the number of generated reads is too large for assembly. input: reference + parameter output: ./1.fastq/reads.fastq assemly.pl assemble the reads (./1.fastq/reads.fastq) from those designed libraries to assemblies. based on the parameters specified in CONFIG file. It will generate assmblies with different K-mer (./2.assembly/*), and choose the assembly with largest n50. Finally, it will produce a quartile summary and mummerplot for each for you to select a good parameter combination. ... -
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TriageTools
Tools for partitioning and prioritizing fastq data
TriageTools is a collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets. The project wiki contains usage information. -
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fqzcomp
A fastq compression program
Fqzcomp is a basic fastq compressor, designed primarily for high performance. Despite that it is comparable to bzip2 for compression levels. -
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Bycom
Bycom can do methylcytosine calling (5mC calling) from BS-seq.
Bycom can do methylcytosine calling from BS-seq (WGBS and RRBS), and either unmapped reads (FASTQ) or mapped reads (SAM/BAM) could be permitted for the input data. Certain SNPs (C>A/G) can also be selected in the output. 1. There's no softwares or methods identify methylcytosines considering the cell heterozygosis caused by multicellular sequencing. Bycom introduced it along with the sequencing errors and unconverson rate based on the Bayesian model. 2. -
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caplib
Correct, translate and analyze combinatorial library sequencing data
Originally developped to handle PacBio CCS data for an AAV capsid library. This program will extract, correct, translate and analyze the sequencng data, starting from the CCS fastq file. -
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DimerRemover
Remove adapter dimers from NGS data
This program can be used to count or remove adapter dimers in fastq files. Using a provided adapter sequence, it generates variations of this sequence and stores them in a hash table. The reads can then be directly matched against the hash. It is far more time efficient than doing alignment. -
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trimMate is a tool to remove junction adapters as well as sequencing adapters from mate pair libraries and trim the sequences accordingly. It works on fastq files generated by next generation sequencing (NGS) machines. The release is source code only, please download from version control.
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QualComp
Lossy Compression algorithm for Quality Scores
QualComp is a lossy compression algorithm for the quality scores presented in a FASTQ file. -
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GenOO-HTS
A Modern Perl Framework for High Throughput Sequencing analysis
GenOO-HTS [jee-noo] is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools. The primary aim of GenOO-HTS is to make simple HTS analyses easy and complicated analyses possible. GenOO-HTS models biological entities into Perl objects and provides relevant attributes and methods that allow for the manipulation of high throughput sequencing data. Using GenOO-HTS as a core development module reduces the overhead... -
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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FusionFinder
Tool to find gene fusions in RNA-Seq data
This software takes FASTQ data from RNA-Seq projects and interrogates it for the presence of gene fusions. -
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fastqsqueeze
compresses all FASTQ files
compresses all FASTQ files as described in http://en.wikipedia.org/wiki/FASTQ_format with a better ratio then zip or standard packers -
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quip
Absurdly high compression of FASTQ sequence files.
Note: this is a mirror of https://github.com/dcjones/quip It may not be entirely up to date. -
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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fqpack
FASTQ compression
Provides bitwise, context-based 2nd generation data compression for large FASTQ-based files -
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NGS-Cleaner is an application that provides cleaning of FASTQ/A formatted large DNA sequence files containing multiple short-reads sequences provided by Next Generation Sequencing platforms.
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Web-based user interface for MAQ (Mapping and Assembly with Qualities), an Illumina / Solexa Deep Sequencing Reads (fastq format) mapping software. MAQGene classifies each found mutation based on its canonically predicted effect on the coding sequence.
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A perl script that converts Illumina qseq files into Phred fastq files for use in Maq. Originally written by Tyler Bachman from UC Riverside, adapted by Eugene Goltsman. Freely available under the terms of GNU GPLv3.
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Paired Sequence File Comparison
Fast validation of FASTQ files containing paired-end reads
For a summary and user's guide, please see the Wiki page: https://sourceforge.net/p/psfc/wiki/Home/ The Wiki page can also be accessed via the top toolbar.
