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"author": "Bianca St\u00f6cker",
"author_email": "bianca.stoecker@uni-due.de",
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"Development Status :: 5 - Production/Stable",
"Environment :: Console",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Programming Language :: Python :: 3",
"Topic :: Scientific/Engineering :: Bio-Informatics"
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"description": "README\n======\n\nSimLoRD - Simulate long Read Data\n---------------------------------\n\nSimLoRD is a read simulator for third generation sequencing reads and is\ncurrently focused on the Pacific Biosciences SMRT error model.\n\nReads are simulated from both strands of a provided or randomly\ngenerated reference sequence.\n\nFeatures\n~~~~~~~~\n\n- The reference can be read from a FASTA file or randomly generated\n with a given GC content. It can consist of several chromosomes, whose\n structure is respected when drawing reads. (Simulation of genome\n rearrangements may be incorporated at a later stage.)\n- The read lengths can be determined in four ways: drawing from a\n log-normal distribution (typical for genomic DNA), sampling from an\n existing FASTQ file (typical for RNA), sampling from a a text file\n with integers (RNA), or using a fixed length\n- Quality values and number of passes depend on fragment length.\n- Provided subread error probabilities are modified according to number\n of passes\n- Outputs reads in FASTQ format and alignments in SAM format\n\nSystem requirements\n~~~~~~~~~~~~~~~~~~~\n\n- `python3 `__\n- `scipy `__\n- `numpy `__\n- `pysam `__\n- `dinopy `__\n\nWe recommend using\n`miniconda `__ and\ncreating an environment for SimLoRD\n\n::\n\n # Create and activate a new environment called simlord\n conda create -n simlord python=3 pip numpy scipy cython\n source activate simlord\n\n # Install packages that are not available with conda from pip\n pip install pysam\n pip install dinopy\n pip install simlord\n\n # You now have a 'simlord' script; try it:\n simlord --help\n\n # In case of a new version update as follows:\n pip install simlord --upgrade \n\n # To switch back to your normal environment, use\n source deactivate\n\nPlatform support\n~~~~~~~~~~~~~~~~\n\nSimLoRD is a pure Python program. This means that it runs on any\noperating system (OS) for which Python 3 and the other packages are\navailable.\n\nExample usage\n~~~~~~~~~~~~~\n\n**Example 1:** Simulate 10000 reads for the reference ref.fasta, use the\ndefault options for simulation and store the reads in ``myreads.fastq``\nand the alignment in ``myreads.sam``.\n\n\n::\n\n simlord --read-reference ref.fasta -n 10000 myreads\n\n\n**Example 2:** Generate a reference with 10 mio bases GC content 0.6\n(i.e., probability 0.3 for both C and G; thus 0.2 probability for both A\nand T), store the reference as random.fasta, and simulate 10000 reads\nwith default options, store reads as ``myreads.fastq``, do not store\nalignments.\n\n::\n\n simlord --generate-reference 0.6 10000000 --save-reference random.fasta\\\n -n 10000 --no-sam myreads\n\n\n**Example 3:** Simulate reads from the given ``reference.fasta``, using\na fixed read length of 5000 and custom subread error probabilities (12%\ninsertion, 12% deletion, 2% substitution). As before, save reads as\n``myreads.fastq`` and ``myreads.sam``.\n\n::\n\n simlord --read-reference reference.fasta -n 10000 -fl 5000\\\n -pi 0.12 -pd 0.12 -ps 0.02 myreads\n\n\nA full list of parameters, as well as their documentation, can be found `here `__.\n\nLast Changes\n~~~~~~~~~~~~\n\n**Version 1.0.2 (2017-03-17)**\n\n*New Features*\n\n- Draw chromosomes for reads weighted with their length instead of equal distributed. This leads to a equal distributed read coverage over the chromosomes. Previous behaviour with equal probabilities for each chromosome can be activated with parameter --uniform-chromosome-probability.\n\n- Parameter --coverage: Determine number of reads depending on the desired read coverage of the whole reference genome.\n\n- Parameter --without-ns: Sample the reads only from regions completly without Ns.\n\nWarning: Using --without-ns may lead to biased read coverage depending on the size of contigs without Ns and the expected readlength.\n\n*Bugs fixed*\n\n- CIGAR string had sometimes wrong count of last match because of false extension after deletion.\n\n\n**Version 1.0.1 (2017-01-03)**\n\n*Bugs fixed*\n\n- Removed nargs=1 at parameter --probability-threshold leading to an error when changing the parameter.\n\n**Version 1.0.0 (2016-07-13)**\n\n*API Changes*\n\n- Changed SEQ in SAM file to reverse complemented read instead of the original read for reads mapping to the reverse complement of the reference.\n\nExample:\n::\n\n reference ATCG read CAAT\n true alignment ||X|\n ATTG\n\n Before: SEQ CAAT and CIGAR string 2=1X1=\n Now: SEQ ATTG and CIGAR string 2=1X1=\n\n\nLicense\n~~~~~~~\n\nSimLoRD is Open Source and licensed under the `MIT\nLicense `__.",
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