SLR-superscaffolder
A scaffold assembling pipeline for stLFR reads.
File Explorer
- conf.ini
- filter.small.r1.fq.gz
- filter.small.r2.fq.gz
- README.md
- scaffold_1.soap.contig
- scaffold_1.soap.ContigIndex
- .gitignore
- __common_function.sh
- clean_prepare.m4
- conf.ini
- prepare.sh
- run.sh
- step_1_prepare_info.m4
- step_2_order.m4
- step_3_orientation.m4
- step_4_pe_fill.m4
- step_5_gapsize.m4
- step_6_gen_seq.m4
- stLFR_barcode_split
- ContigBinBarcode.cpp
- ContigBinBarcode.h
- ContigOrder.h
- contigPEGraph.h
- EasySam.h
- ScaffInfo.cpp
- ScaffInfo.h
- stLFRRead.h
- BinCluster.cpp
- ChopBin.cpp
- FakeSOAPContig.cpp
- FillTrunkByPE.cpp
- GapSize.cpp
- Makefile
- MST.cpp
- Orientation.cpp
- ParseReadName.cpp
- PEGraph.cpp
- README.md
- Sam2ReadOnContig.cpp
- ScaffInfo2Seq.cpp
- SeedCluster.cpp
- SplitInfo.cpp
- StaticsticUnique.cpp
- test.cpp
- Trunk2ScaffInfo.cpp
- agp.cpp
- agp.h
- agp_test.cpp
- argsparser.cpp
- argsparser.h
- argsparser_test.cpp
- collection.h
- collection_test.cpp
- .gitignore
- file_reader.cpp
- file_reader.h
- file_test.cpp
- file_writer.cpp
- file_writer.h
- gzstream.cpp
- gzstream.h
- fib_heap.h
- fib_heap_test.cpp
- MinTree.h
- MinTree_test.cpp
- DisJointSet.h
- DisJointSet_test.cpp
- GraphBasic.h
- GraphBasic_test.cpp
- GraphTipRemove.h
- GraphTipRemove_test.cpp
- incr_array.h
- incr_array_test.cpp
- Interval.h
- Interval_test.cpp
- Linear.h
- Linear_test.cpp
- log.cpp
- log.h
- log_test.cpp
- contigIndex.cpp
- contigIndex.h
- Error.h
- fileName.h
- flags.h
- freq.h
- mapHelper.h
- misc_test.cpp
- TagId.cpp
- TagId.h
- MultiThread.h
- MultiThread_test.cpp
- stringtools.cpp
- stringtools.h
- stringtools_test.cpp
- Test.h
- README.md
- .gitignore
- Makefile
- .gitignore
- .gitmodules
- image.png
- install.sh
- LICENSE
- README.md
# Use via CDN
jsDelivrjsDelivr serves any public GitHub repository as a CDN with zero setup. Pick a version and a file to get a ready-to-paste link and snippet.
Command Glossary
Commands referenced in this DOCs, explained below.
git clone
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git clone
Clone an existing repository.
git clone {{remote_repository_location}} {{path/to/directory}}
Clone an existing repository into a new directory (the default directory is the repository name):
git clone --recursive {{remote_repository_location}}
Clone an existing repository and its submodules:
git clone {{[-n|--no-checkout]}} {{remote_repository_location}}
Clone only the `.git` directory of an existing repository:
git submodule
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git submodule
Inspect, update, and manage submodules.
git submodule
View existing submodules and the checked-out commit for each one:
git submodule update --init --recursive
Install a repository's submodules (listed in `.gitmodules`):
git submodule add {{repository_url}}
Add a Git repository as a submodule of the current one:
vim
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vim
Vim (Vi IMproved), a command-line text editor, provides several modes for different kinds of text manipulation.
Pressing `<i>` in normal mode enters insert mode. Pressing `<Esc>` goes back to normal mode, which enables the use of Vim commands.
See also: `vimdiff`, `vimtutor`, `nvim`, `gvim`.
vim {{path/to/file}}
Open a file:
vim +{{line_number}} {{path/to/file}}
Open a file at a specified line number:
<:>help<Enter>
View Vim's help manual: