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自带

* Celera Assembler
* [jellyfish](https://github.com/gmarcais/Jellyfish): k-mer counting
* prepare: 无文档, 看起来是预处理数据用的.
* [Quorum](https://github.com/gmarcais/Quorum): Error correction for Illumina reads.
* samtools
* SOAPdenovo2
* SuperReads: masurca 的主程序. 这个是我们所需要的, 合并 reads 的功能就在这里. 源码约五万行.
* ufasta: UMD 的操作 fasta 的工具, 未在其它地方发现相关信息. 里面的 tests 写得不错, 值得借鉴.

# 安装

```bash
echo "==> MaSuRCA"
cd /prepare/resource/
wget -N ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA-3.1.3.tar.gz

if [ -d $HOME/share/MaSuRCA ]; then
    rm -fr $HOME/share/MaSuRCA
fi

cd $HOME/share/
tar xvfz /prepare/resource/MaSuRCA-3.1.3.tar.gz

mv MaSuRCA-* MaSuRCA
cd MaSuRCA
sh install.sh
```

编译完成后, 会生成 `bin` 目录, 里面是可执行文件, `tree bin`.

```text
bin
├── add_missing_mates.pl
├── addSurrogatesToFrgCtgFile
├── addSurrogatesToFrgctg.perl
├── bloom_query
├── closeGapsInScaffFastaFile.perl
├── closeGapsLocally.perl
├── closeGaps.oneDirectory.fromMinKmerLen.perl
├── closeGaps.oneDirectory.perl
├── closeGaps.perl
├── close_gaps.sh
├── collectReadSequencesForLocalGapClosing
├── compute_sr_cov.pl
├── compute_sr_cov.revisedForGCContig.pl
├── create_end_pairs.perl
├── create_end_pairs.pl
├── createFastaSuperReadSequences
├── createKUnitigMaxOverlaps
├── create_k_unitigs_large_k
├── create_k_unitigs_large_k2
├── create_sr_frg
├── create_sr_frg.pl
├── createSuperReadSequenceAndPlacementFileFromCombined.perl
├── createSuperReadsForDirectory.perl
├── eliminateBadSuperReadsUsingList
├── error_corrected2frg
├── expand_fastq
├── extendSuperReadsBasedOnUniqueExtensions
├── extendSuperReadsForUniqueKmerNeighbors
├── extractJoinableAndNextPassReadsFromJoinKUnitigs.perl
├── extractreads_not.pl
├── extractreads.pl
├── extract_unjoined_pairs.pl
├── fasta2frg_m.pl
├── fasta2frg.pl
├── filter_alt.pl
├── filter_library.sh
├── filter_overlap_file
├── filter_redundancy.pl
├── finalFusion
├── findMatchesBetweenKUnitigsAndReads
├── findReversePointingJumpingReads_bigGenomes.perl
├── findReversePointingJumpingReads.perl
├── fix_unitigs.sh
├── getATBiasInCoverageForIllumina_v2
├── getEndSequencesOfContigs.perl
├── getGCBiasStatistics.perl
├── getLengthStatisticsForKUnitigsFile.perl
├── getMeanAndStdevByGCCount.perl
├── getMeanAndStdevForGapsByGapNumUsingCeleraAsmFile.perl
├── getMeanAndStdevForGapsByGapNumUsingCeleraTerminatorDirectory.perl
├── getNumBasesPerReadInFastaFile.perl
├── getSequenceForClosedGaps.perl
├── getSequenceForLocallyClosedGaps.perl
├── getSuperReadInsertCountsFromReadPlacementFile
├── getSuperReadInsertCountsFromReadPlacementFileTwoPasses
├── getSuperReadPlacements.perl
├── getUnitigTypeFromAsmFile.perl
├── homo_trim
├── jellyfish
├── joinKUnitigs_v3
├── killBadKUnitigs
├── makeAdjustmentFactorsForNumReadsForAStatBasedOnGC
├── makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2
├── masurca
├── MasurcaCelera.pm
├── MasurcaCommon.pm
├── MasurcaConf.pm
├── MasurcaSoap.pm
├── masurca-superreads
├── MasurcaSuperReads.pm
├── mergeSuperReadsUniquely.pl
├── outputAlekseysJellyfishReductionFile.perl
├── outputJoinedPairs.perl
├── outputMatedReadsAsReverseComplement.perl
├── outputRecordsNotOnList
├── parallel
├── putReadsIntoGroupsBasedOnSuperReads
├── quorum
├── quorum_create_database
├── quorum_error_correct_reads
├── recompute_astat_superreads.sh
├── reduce_sr
├── rename_filter_fastq
├── rename_filter_fastq.pl
├── reportReadsToExclude.perl
├── restore_ns.pl