パッケージ: reapr (1.0.18+dfsg-6)
universal tool for genome assembly evaluation
REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.
The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly.
その他の reapr 関連パッケージ
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- dep: bamtools
- BAM（ゲノムアラインメント）ファイルの操作用ツール
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- dep: libbamtools2.5.2 (>= 2.5.2+dfsg)
- dynamic library for manipulating BAM (genome alignment) files
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- dep: libc6 (>= 2.34)
- GNU C ライブラリ: 共有ライブラリ
以下のパッケージによって提供される仮想パッケージでもあります: libc6-udeb
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- dep: libfile-copy-link-perl
- Perl extension for replacing a link by a copy of the linked file
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- dep: libgcc-s1 (>= 3.0)
- GCC 共有ライブラリ
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- dep: libstdc++6 (>= 13.1)
- GNU 標準 C++ ライブラリ v3
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- dep: libtabixpp0t64 (>= 1.0.0)
- C++ wrapper to tabix indexer
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- dep: r-base
- GNU R 統計計算・グラフィックスシステム
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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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- dep: snpomatic
- fast, stringent short-read mapping software
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- dep: tabix
- generic indexer for TAB-delimited genome position files