Moderator: shenwei356
shenwei356 ♦ 4.5k
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Posts by shenwei356
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... Just for given sample data.
```
$ sed 's/^>//' headers.txt | perl -pne 's/(\w+_\w+)_/$1\t/' > headers.tsv
$ cat headers.tsv
NZ_CP023010 Elizabethkingia anophelis FDAARGOS_198
NZ_MRWY01000004 Klebsiella michiganensis_CAV1755
$ seqkit replace -p '^(.+?)\..+_' -k headers.tsv -r '{kv}_' ...
written 20 hours ago by
shenwei356 ♦ 4.5k
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... ```
$ spades.py --help
SPAdes genome assembler v3.13.0
...
Advanced options:
--dataset file with dataset description in YAML format
-t/--threads number of threads
[default: 16]
-m/--memory RAM limit for SPAdes in Gb (terminat ...
written 21 days ago by
shenwei356 ♦ 4.5k
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... Yes I know, I guess proteins of bacteria in RefSeq are enough for his/her purpose, before knowing for what he/she use the data.
Anyway, one can try
```
# downlaod
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt
# reformat
cat assembly_summary.txt | sed 1d | sed '1s/^# ...
written 25 days ago by
shenwei356 ♦ 4.5k
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... You can also download `.faa.gz` files for every bacterium in [RefSeq](ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria), check [another tutorial](http://blog.shenwei.me/manipulation-on-ncbi-refseq-bacterial-assembly-summary/) ...
written 25 days ago by
shenwei356 ♦ 4.5k
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Comment:
C: Linearize fasta files
... （￣ へ￣ ）Yes, the [patch](https://github.com/lh3/seqtk/pull/123) is worth it. Thank you Fabian for this great patch! ...
written 5 weeks ago by
shenwei356 ♦ 4.5k
2
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2
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272
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2
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Answer:
C: Linearize fasta files
... `seqtk seq input.fa` (1.3-r106 [68752fd](https://github.com/lh3/seqtk/commit/68752fd8497aff82b273b1f7f541b9905760586f)) is faster than `seqkit seq -w 0 input.fa` (v0.10.0) in my test on both SSD and HDD.
Version:
- seqkit [v0.10.0](https://github.com/shenwei356/seqkit/releases/tag/v0.10.0)
- seqtk ...
written 5 weeks ago by
shenwei356 ♦ 4.5k
1
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... [seqkit subseq](https://bioinf.shenwei.me/seqkit/usage/#subseq) supports this, if you want a fast solution.
seqkit subseq -r -1000:-1 seqs.fa > result.fa
If you want to learn programming, write some Python scripts using Biopython. ...
written 6 weeks ago by
shenwei356 ♦ 4.5k
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170
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... seems datamash can with `perc` operation. https://www.gnu.org/software/datamash/manual/datamash.html ...
written 7 weeks ago by
shenwei356 ♦ 4.5k
1
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170
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... It's simple: sorting by length, calculating q10 and q90, and retrieving seqs in this range.
# Step 1
# Getting total number
n=$(seqkit stats test.fa -T | sed 1d | cut -f 4)
# Step 2, option A
# "seqkit sort -l" needs unique headers.
# "seqkit range" retrieve records in ...
written 7 weeks ago by
shenwei356 ♦ 4.5k
0
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1
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188
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1
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... Just google and install GNU grep ~~
[How to install and use GNU Grep in OSX](https://apple.stackexchange.com/questions/193288/how-to-install-and-use-gnu-grep-in-osx) ...
written 8 weeks ago by
shenwei356 ♦ 4.5k
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