eLxr packages [ bianca ]
[ ソース: iva ]
パッケージ: iva (1.0.11+ds-6)
iterative virus sequence assembler
IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth.
IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence.
その他の iva 関連パッケージ
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- dep: default-jre-headless
- Standard Java or Java compatible Runtime (headless)
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- dep: fastaq
- FASTA and FASTQ file manipulation tools
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- dep: kmc
- count kmers in genomic sequences
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- dep: mummer
- Efficient sequence alignment of full genomes
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- dep: perl
- Larry Wall's Practical Extraction and Report Language
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- dep: python3
- interactive high-level object-oriented language (default python3 version)
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- dep: python3-networkx
- tool to create, manipulate and study complex networks (Python3)
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- dep: python3-numpy
- Python library for numerical computations (Python 3)
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- dep: python3-packaging
- core utilities for python3 packages
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- dep: python3-pysam
- interface for the SAM/BAM sequence alignment and mapping format (Python 3)
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- dep: samtools
- processing sequence alignments in SAM, BAM and CRAM formats
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- dep: smalt
- Sequence Mapping and Alignment Tool
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- rec: bioperl
- Perl tools for computational molecular biology
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- rec: r-base-core
- GNU R core of statistical computation and graphics system
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- rec: trimmomatic
- flexible read trimming tool for Illumina NGS data