Shannon

RNA-Seq

This GitHub repostitory contains the code and the website for the Shannon assembly project is here: http://sreeramkannan.github.io/Shannon/

Name	Name	Last commit message	Last commit date
Latest commit olivomao issue19: add non-default python/shannon path for rc_gnu in shannon.py May 10, 2017 30a8619 · May 10, 2017 History 250 Commits
BACKUP	BACKUP	1. Find reverse complement fast	Mar 30, 2016
Samples	Samples	reads written into memory before writing into file. Max_files_open er…	Feb 25, 2016
__pycache__	__pycache__	rebridging disabled, and default mate pair parameter fixed	Oct 29, 2015
testSuite	testSuite	MAJOR UPGRADE	Jan 12, 2016
.DS_Store	.DS_Store	updated with comments	Sep 25, 2015
README.md	README.md	Update README.md	Aug 15, 2016
algorithm_SF.py	algorithm_SF.py	Algorithm_SF updated	Sep 8, 2016
ext_corr.py	ext_corr.py	1. Find reverse complement fast	Mar 30, 2016
extension_correction.py	extension_correction.py	modi polyA into lowComplexity to avoid load low complexity kmers	May 2, 2017
extension_correction_Kminus1.py	extension_correction_Kminus1.py	error in extension_correction_Kminus1 fixed	Mar 3, 2016
fast_reps.py	fast_reps.py	fast_reps default r increased from 12 to 18. This should increase spe…	Feb 27, 2016
faster_reps.py	faster_reps.py	Many major changes	Mar 26, 2016
filter_FP.py	filter_FP.py	filtering FP threshold updated in filter_FP to 0.9	Jul 7, 2016
filter_FP_2s.py	filter_FP_2s.py	filter_FP_2s added	Sep 3, 2016
filter_kallisto.py	filter_kallisto.py	Typos corrected	Sep 13, 2016
filter_trans.py	filter_trans.py	New files	Sep 16, 2015
find_reps_blat.py	find_reps_blat.py	More edits	Feb 2, 2016
kmers_for_component.py	kmers_for_component.py	Typos fixed	Sep 10, 2016
kmers_for_component_back.py	kmers_for_component_back.py	Split into NR, read, RC in parallel, split, write to file every NR chunk	Jun 9, 2016
kp1mer_to_kmer.py	kp1mer_to_kmer.py	Added transcript filtering along with other options	Feb 1, 2016
manual.md	manual.md	MAJOR UPGRADE	Jan 12, 2016
mbgraph.py	mbgraph.py	node copy counts updated	Sep 7, 2016
multibridging.py	multibridging.py	multibriding updated to read in reads in FF orientation	May 30, 2016
parallel_blat.py	parallel_blat.py	New files	Sep 16, 2015
parallel_blat_python.py	parallel_blat_python.py	tabspace corrected	Mar 31, 2016
path_decompose_sparse.py	path_decompose_sparse.py	1. Find reverse complement fast	Mar 30, 2016
process_concatenated_fasta.py	process_concatenated_fasta.py	process_concatenated_fasta updated	Sep 7, 2016
rc_gnu.py	rc_gnu.py	Read length finding: Typos corrected	Sep 13, 2016
rc_s.py	rc_s.py	GNU parallel to Python parallelization	Sep 10, 2016
run_MB_SF.py	run_MB_SF.py	GNU Parallel NO LONGER required.	Mar 31, 2016
run_MB_SF_fn.py	run_MB_SF_fn.py	typos	Jun 1, 2016
run_parallel_cmds.py	run_parallel_cmds.py	inMem mode added. Further testing needed. Does not respect nJobs curr…	May 19, 2016
run_quorum.py	run_quorum.py	error in processing --ss corrected. The flag -p was not fed correctly…	Mar 15, 2016
shannon.py	shannon.py	issue19: add non-default python/shannon path for rc_gnu in shannon.py	May 10, 2017
temp	temp	Added transcript filtering along with other options	Feb 1, 2016
test.py	test.py	Split into NR, read, RC in parallel, split, write to file every NR chunk	Jun 9, 2016
test_suite.py	test_suite.py	test Suite	Jan 29, 2016
tester.py	tester.py	FP lines added	Jul 8, 2016
trie.py	trie.py	New files	Sep 16, 2015
weight_updated_graph.py	weight_updated_graph.py	parameter ordering error in weight_updated_graph corrected	Mar 2, 2016

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