Results for "SV"
Bio-Scripts
(JitMetaENV) ➜ ~ conda install -c bioconda quast Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer vers...1208 days ago
- (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen...
1208 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
...ject src/CMakeFiles/i-visualize.dir/SvgWriter.cpp.o [ 32%] Building...home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp: In member functio.../wgd/./testset/datasetII/alignment.csv -- Installing: /home/urbe/an...rath_2_3_beta/AlignmentMultiplicon2.svg -- Installing: /home/urbe/a...1197 days ago
- vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda csvtk Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.
1048 days ago
- ...ra-utils texlive-latex-recommended texlive-latex-extra texinfo gir1.2-rsvg-2.0 The following NEW packa...eroot (1.22-2ubuntu1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot...
1048 days ago
Tadpole is 250x faster than SPADes assembler !
...ity graph (partially implemented) dump= Write kmers and their counts. fastadump=t Write kmers and counts as fasta versus 2-column tsv. mincounttodump=1 Only du...969 days ago
Run Pango on your multifasta file !
.../envs/pangolin/lib/python3.8/site-packages/pangoLEARN/data/lineages.hash.csv Job stats: job...:09 Output file written to: /home/jnarayan/RF_DATA/FASTA/lineage_report.csv (pangolin) [jnarayan@hn1 FAS...881 days ago
bash script to extract sequence by ids !
...00.3.1 ACGTACGTACGTACGTACGTACG EOF cat > gene_ids.txt ids_gene_ids.tsv # Select ids that correspond to the desired gene ids: grep -f gene_ids.txt ids_gene_ids.tsv | cut -f1 > ids.selected.txt...817 days ago
- #Commands to run PERF PERF --format fasta -t 30 -i reference.fasta -o PERF_output.tsv --include-atomic -m 2 -M 7 -l 12
785 days ago
Bash command to explore assembly summary genbank !
wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt pip3 install csvkit csvcut -t -K 1 -c 'excluded_from_refseq' assembly_summary_genbank.txt \ | tail -n +2 | tr ";" "\n" \ | sed -e 's/^ //' -e 's/ $//' | grep -v '""' \ | sort | uniq -c | sort -nr762 days ago
