Owner
shenwei356
9 indexed repositories · View on GitHub
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seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Go · 1593 stars
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csvtk
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
Go · 1170 stars
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rush
A cross-platform command-line tool for executing jobs in parallel
Go · 1134 stars
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awesome
Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.
768 stars
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taxonkit
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
Go · 481 stars
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LexicMap
LexicMap: efficient sequence alignment against millions of prokaryotic genomes
Go · 227 stars
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kmcp
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
Go · 222 stars
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gtdb-taxdump
GTDB taxonomy taxdump files with trackable TaxIds
R · 63 stars
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taxid-changelog
NCBI taxonomic identifier (taxid) changelog, including taxids deletion, new adding, merge, reuse, and rank/name changes.
R · 28 stars
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Difficulty 5/5 Over a week Newbie friendliness 35/100
shenwei356/LexicMap#35 · 1 comment ·
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Difficulty 4/5 3-5 days Newbie friendliness 35/100
shenwei356/awesome#20 ·
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Difficulty 5/5 Over a week Newbie friendliness 30/100
shenwei356/taxonkit#125 · 2 comments ·
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Difficulty 5/5 Over a week Newbie friendliness 20/100
shenwei356/LexicMap#29 · 2 comments ·
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Difficulty 5/5 Over a week Newbie friendliness 25/100
shenwei356/LexicMap#27 · 5 comments ·
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Difficulty 4/5 3-5 days Newbie friendliness 25/100
shenwei356/taxonkit#123 · 1 comment ·
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SAM format output? Open
Difficulty 5/5 Over a week Newbie friendliness 30/100
shenwei356/LexicMap#26 · 21 comments ·
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Difficulty 2/5 1-3 hours Newbie friendliness 25/100
shenwei356/kmcp#55 · 1 comment ·
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Difficulty 5/5 Over a week Newbie friendliness 25/100
shenwei356/gtdb-taxdump#9 · 5 comments ·
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Difficulty 4/5 3-5 days Newbie friendliness 25/100
shenwei356/kmcp#54 · 3 comments ·
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Difficulty 5/5 Over a week Newbie friendliness 20/100
shenwei356/kmcp#53 · 1 comment ·
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Difficulty 4/5 3-5 days Newbie friendliness 30/100
shenwei356/taxonkit#111 · 2 comments ·
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Difficulty 4/5 3-5 days Newbie friendliness 35/100
shenwei356/taxonkit#109 · 5 comments ·
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Search optimization Open
Difficulty 5/5 Over a week Newbie friendliness 35/100
shenwei356/kmcp#52 · 2 comments ·
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Difficulty 1/5 Under an hour Newbie friendliness 25/100
shenwei356/LexicMap#10 ·
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Difficulty 1/5 Under an hour Newbie friendliness 35/100
shenwei356/awesome#17 ·
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Difficulty 1/5 Under an hour Newbie friendliness 25/100
shenwei356/kmcp#49 · 2 comments ·
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Difficulty 4/5 3-5 days Newbie friendliness 25/100
shenwei356/kmcp#48 · 4 comments ·
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Difficulty 1/5 Under an hour Newbie friendliness 35/100
shenwei356/kmcp#47 · 1 comment ·
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TODO list Open
Difficulty 5/5 Over a week Newbie friendliness 25/100
shenwei356/LexicMap#5 · 2 comments ·
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Difficulty 1/5 Under an hour Newbie friendliness 35/100
shenwei356/kmcp#46 · 3 comments ·
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Difficulty 4/5 3-5 days Newbie friendliness 35/100
shenwei356/seqkit#477 · 4 comments ·
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Difficulty 5/5 Over a week Newbie friendliness 28/100
shenwei356/seqkit#475 · 4 comments · 1 reaction ·
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Difficulty 5/5 Over a week Newbie friendliness 20/100
shenwei356/kmcp#45 · 4 comments ·
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Difficulty 5/5 Over a week Newbie friendliness 25/100
shenwei356/kmcp#44 · 6 comments ·
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enhancement new feature
Difficulty 3/5 1-2 days Newbie friendliness 45/100
shenwei356/taxonkit#93 · 6 comments ·
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enhancement
Difficulty 4/5 3-5 days Newbie friendliness 25/100
shenwei356/seqkit#443 · 5 comments ·
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Difficulty 4/5 3-5 days Newbie friendliness 25/100
shenwei356/taxonkit#91 · 5 comments ·
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Difficulty 4/5 3-5 days Newbie friendliness 25/100
shenwei356/gtdb-taxdump#8 · 6 comments ·
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new feature
Difficulty 4/5 3-5 days Newbie friendliness 38/100
shenwei356/taxonkit#88 · 3 comments ·
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Difficulty 5/5 Over a week Newbie friendliness 25/100
shenwei356/kmcp#40 · 3 comments ·
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Difficulty 5/5 Over a week Newbie friendliness 20/100
shenwei356/kmcp#38 · 9 comments ·
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Difficulty 5/5 Over a week Newbie friendliness 25/100
shenwei356/taxonkit#86 · 3 comments ·
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Difficulty 3/5 1-2 days Newbie friendliness 35/100
shenwei356/kmcp#35 · 2 comments ·
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database work-in-progress
Difficulty 5/5 Over a week Newbie friendliness 15/100
shenwei356/kmcp#29 · 2 comments ·
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Difficulty 5/5 Over a week Newbie friendliness 25/100
shenwei356/kmcp#28 · 2 comments ·
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documentation
Difficulty 4/5 3-5 days Newbie friendliness 15/100
shenwei356/kmcp#27 · 2 comments ·
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add-tutorial
Difficulty 5/5 Over a week Newbie friendliness 20/100
shenwei356/gtdb-taxdump#7 · 6 comments ·
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Difficulty 5/5 Over a week Newbie friendliness 15/100
shenwei356/gtdb-taxdump#6 · 3 comments ·
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Silva database? Open
Difficulty 5/5 Over a week Newbie friendliness 20/100
shenwei356/gtdb-taxdump#5 · 14 comments ·
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bug
Difficulty 3/5 1-2 days Newbie friendliness 35/100
shenwei356/gtdb-taxdump#2 · 22 comments ·
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Difficulty 4/5 3-5 days Newbie friendliness 35/100
shenwei356/taxonkit#59 · 2 comments ·
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Automatically disable ambiguous-matches correction for complex communities with thousands of species Openenhancement
Difficulty 4/5 3-5 days Newbie friendliness 35/100
shenwei356/kmcp#13 ·
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add older taxdumps? Open
Difficulty 3/5 1-2 days Newbie friendliness 25/100
shenwei356/taxid-changelog#2 · 2 comments ·
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enhancement low priority
Difficulty 4/5 3-5 days Newbie friendliness 35/100
shenwei356/csvtk#172 · 8 comments · 2 reactions ·
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Update benchmarks Open
Difficulty 2/5 1-3 hours Newbie friendliness 35/100
shenwei356/taxonkit#47 ·
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enhancement
Difficulty 4/5 3-5 days Newbie friendliness 38/100
shenwei356/seqkit#191 · 5 comments ·
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enhancement
Difficulty 5/5 Over a week Newbie friendliness 25/100
shenwei356/seqkit#177 · 2 comments · 2 reactions ·
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Difficulty 5/5 Over a week Newbie friendliness 20/100
shenwei356/taxid-changelog#1 · 1 comment ·