Search results for "Bio::Seq::Quality"
Bio::Seq::Quality - Implementation of sequence with residue quality and trace values
This object stores base quality values together with the sequence string. The implementation is based on Bio::Seq::Meta::Array. qual() and trace() are base methods to store and retrieve information that have extensions to retrieve values as a scalar ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::Seq::QualI - Interface definition for a Bio::Seq::Qual
- Bio::Seq::TraceI - Interface definition for a Bio::Seq::Trace
- Bio::DB::Qual - Fast indexed access to quality files
- 15 more results from BioPerl »
FAST::Bio::Seq::Quality - Implementation of sequence with residue quality and trace values
This object stores base quality values together with the sequence string. It is a reimplementation of Chad Matsalla's FAST::Bio::Seq::SeqWithQuality module using FAST::Bio::Seq::MetaI. The implementation is based on FAST::Bio::Seq::Meta::Array. qual(...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::Seq::QualI - Interface definition for a FAST::Bio::Seq::Qual
- FAST::Bio::Seq::TraceI - Interface definition for a FAST::Bio::Seq::Trace
- FAST::Bio::SeqIO::scf - .scf file input/output stream
- 16 more results from FAST »
bam2wig.pl - A program to convert Bam alignments into a wig representation file.
This program will enumerate aligned sequence tags and generate a wig, or optionally BigWig, file. Alignments may be counted and recorded in several different ways. Strict enumeration may be performed and recorded at either the alignment's start or mi...
TJPARNELL/Bio-ToolBox-1.691 - 13 Oct 2022 18:07:52 UTC - Search in distribution
fromsam
TSIBLEY/App-RecordStream-Bio-0.24
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04 Aug 2017 17:45:08 UTC
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- App::RecordStream::Bio - A collection of record-handling tools related to biology
Bio::Lite - Lightweight and fast module with a simplified API to ease scripting in bioinformatics
Bio::Lite is a set of subroutines that aims to answer similar questions as Bio-perl distribution in a FAST and SIMPLE way. Bio::Lite does not make use of complexe data struture, or objects, that would lead to a slow execution. All methods can be impo...
JAUDOUX/Bio-Lite-0.003 - 23 Jul 2014 16:15:45 UTC - Search in distribution
Bio::fastAPD - rapid calculation of average pairwise difference (APD) for multiple sequence alignments
The Bio::fastAPD module provides a computationally efficient method for the calculation of average pairwise difference (APD), a measure of nucleotide diversity, from multiple sequence alignment (MSA) data. This module also provides rapid standard err...
JDBAUGHER/Bio-fastAPD-1.10.0 - 08 Apr 2015 20:59:21 UTC - Search in distribution
Bio::DB::HTS - Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
This module provides a Perl interface to the HTSlib library for indexed and unindexed SAM/BAM/CRAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information a...
AVULLO/Bio-DB-HTS-3.01 - 23 Apr 2019 13:51:11 UTC - Search in distribution- Bio::DB::HTS::Alignment - The HTS alignment object
- Bio::DB::HTS::Query - Object representing the query portion of a BAM/SAM alignment
- Bio::DB::HTS::Kseq::Record - Entry from a Kseq iterator
Bio::DB::Sam - Read SAM/BAM database files
This module provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across...
LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC - Search in distribution- Bio::DB::Bam::Alignment - The SAM/BAM alignment object
- Bio::DB::Bam::Query - Object representing the query portion of a BAM/SAM alignment
FASTX::Abi - Read Sanger trace file (chromatograms) in FASTQ format. For traces called with hetero option, the ambiguities will be split into two sequences to allow usage from NGS tools that usually do not understand IUPAC ambiguities.
PROCH/FASTX-Abi-1.0.1
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11 Nov 2021 16:19:58 UTC
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Bio::ViennaNGS - A Perl distribution for Next-Generation Sequencing (NGS) data analysis
Bio::ViennaNGS is a distribution of Perl modules and utilities for building efficient Next-Generation Sequencing (NGS) analysis pipelines. It covers various aspects of NGS data analysis, including (but not limited to) conversion of sequence annotatio...
MTW/Bio-ViennaNGS-v0.19.2 - 11 Dec 2018 13:25:00 UTC - Search in distribution
Bio::Grep::Cookbook - Bio::Grep Cookbook
This collection of recipes intends to provide you solutions for the most common problems and to make the development process easier....
LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC - Search in distribution- Bio::Grep::SearchSettings - Data structure for all search settings
- Bio::Grep::Backend::GUUGle - GUUGle back-end
- Bio::Grep::Backend::BackendI - Superclass for all back-ends
- 1 more result from Bio-Grep »
CracTools::Utils - A set of useful functions
Bio::Lite is a set of subroutines that aims to answer similar questions as Bio-perl distribution in a FAST and SIMPLE way. Bio::Lite does not make use of complexe data struture, or objects, that would lead to a slow execution. All methods can be impo...
JAUDOUX/CracTools-1.251 - 09 Jun 2017 15:29:56 UTC - Search in distribution
Bio::SeqReader::Fastq - Class providing a reader for files in FASTQ format.
Bio::SeqReader::Fastq provides a method for reading a file or stream in FASTQ format. This format is described in P. J. A. Cock, C. J. Fields, N. Goto, M. L. Heuer, P. M. Rice. (2010) *The Sanger FASTQ file format for sequences with quality scores, a...
JAC/Bio-SeqReader-0.1.3 - 25 Sep 2012 04:13:30 UTC - Search in distribution- Bio::SeqReader::FastqRecord - Class providing methods for representing header, sequence, and quality information in FASTQ records.
Bio::Graphics::Glyph::hybrid_plot - An xyplot plot drawing dual graph using data from two or more wiggle files per track
Note that for full functionality this glyph requires Bio::Graphics::Glyph::generic (generic glyph is used for drawing individual matches for small RNA alignments at a high zoom level, specified by semantic zooming in GBrowse conf file) Unlike the reg...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC - Search in distribution