套件：racon（1.3.2-1 以及其他的）
consensus module for raw de novo DNA assembly of long uncorrected reads
Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.
Racon can be used as a polishing tool after the assembly with either Illumina data or data produced by third generation of sequencing. The type of data inputed is automatically detected.
Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files can be compressed with gzip.
Racon can also be used as a read error-correction tool. In this scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps between reads including dual overlaps.
A wrapper script is also available to enable easier usage to the end- user for large datasets. It has the same interface as racon but adds two additional features from the outside. Sequences can be subsampled to decrease the total execution time (accuracy might be lower) while target sequences can be split into smaller chunks and run sequentially to decrease memory consumption. Both features can be run at the same time as well.
其他與 racon 有關的套件
|
|
|
|
-
- dep: libc6 (>= 2.14)
- GNU C 函式庫：共用函式庫
同時作為一個虛擬套件由這些套件填實： libc6-udeb
-
- dep: libedlib0 (>= 1.2.3)
- library for sequence alignment using edit distance
-
- dep: libgcc1 (>= 1:3.0)
- GCC 支援函式庫
-
- dep: libspoa1.1.5 (>= 1.1.3)
- SIMD partial order alignment library
-
- dep: libstdc++6 (>= 7)
- GNU Standard C++ Library v3
-
- dep: libthread-pool0 (>= 1.0.0)
- C++ thread pool library
-
- dep: zlib1g (>= 1:1.2.11.dfsg)
- 壓縮函式庫 - 跑程式時用(runtime)