update doc for v2.0.0

shenwei356 · Aug 26, 2021 · 88c98b1 · 88c98b1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/Dockerfile b/Dockerfile
@@ -24,7 +24,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 #End: install prerequisites
 
 #Begin: install golang
-ENV GOLANG_VERSION 1.11
+ENV GOLANG_VERSION 1.17
 ENV GOLANG_DOWNLOAD_URL https://golang.org/dl/go$GOLANG_VERSION.linux-amd64.tar.gz
 ENV GOLANG_SHA256_CHECKSUM b3fcf280ff86558e0559e185b601c9eade0fd24c900b4c63cd14d1d38613e499
 ENV GOPATH $HOME/go

diff --git a/README-v0.3.1.1.md b/README-v0.3.1.1.md
@@ -0,0 +1,73 @@
+## Introduction
+
+FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and
+protein sequences. Common manipulations of FASTA/Q file include converting,
+searching, filtering, deduplication, splitting, shuffling, and sampling.
+Existing tools only implement some of these manipulations,
+and not particularly efficiently, and some are only available for certain
+operating systems. Furthermore, the complicated installation process of
+required packages and running environments can render these programs less
+user friendly.
+
+This project describes a cross-platform ultrafast comprehensive
+toolkit for FASTA/Q processing. SeqKit provides executable binary files for
+all major operating systems, including Windows, Linux, and macOS, and can
+be directly used without any dependencies or pre-configurations.
+SeqKit demonstrates competitive performance in execution time and memory
+usage compared to similar tools. The efficiency and usability of SeqKit
+enable researchers to rapidly accomplish common FASTA/Q file manipulations.
+
+### Features comparison
+
+|Categories          |Features               |seqkit  |fasta_utilities|fastx_toolkit|pyfaidx|seqmagick|seqtk
+|:-------------------|:----------------------|:------:|:-------------:|:-----------:|:-----:|:-------:|:---:
+|**Formats support** |Multi-line FASTA       |Yes     |Yes            |--           |Yes    |Yes      |Yes
+|                    |FASTQ                  |Yes     |Yes            |Yes          |--     |Yes      |Yes
+|                    |Multi-line  FASTQ      |Yes     |Yes            |--           |--     |Yes      |Yes
+|                    |Validating sequences   |Yes     |--             |Yes          |Yes    |--       |--
+|                    |Supporting RNA         |Yes     |Yes            |--           |--     |Yes      |Yes
+|**Functions**       |Searching by motifs    |Yes     |Yes            |--           |--     |Yes      |--
+|                    |Sampling               |Yes     |--             |--           |--     |Yes      |Yes
+|                    |Extracting sub-sequence|Yes     |Yes            |--           |Yes    |Yes      |Yes
+|                    |Removing duplicates    |Yes     |--             |--           |--     |Partly   |--
+|                    |Splitting              |Yes     |Yes            |--           |Partly |--       |--
+|                    |Splitting by seq       |Yes     |--             |Yes          |Yes    |--       |--
+|                    |Shuffling              |Yes     |--             |--           |--     |--       |--
+|                    |Sorting                |Yes     |Yes            |--           |--     |Yes      |--
+|                    |Locating motifs        |Yes     |--             |--           |--     |--       |--
+|                    |Common sequences       |Yes     |--             |--           |--     |--       |--
+|                    |Cleaning bases         |Yes     |Yes            |Yes          |Yes    |--       |--
+|                    |Transcription          |Yes     |Yes            |Yes          |Yes    |Yes      |Yes
+|                    |Translation            |Yes     |Yes            |Yes          |Yes    |Yes      |--
+|                    |Filtering by size      |Yes     |Yes            |--           |Yes    |Yes      |--
+|                    |Renaming header        |Yes     |Yes            |--           |--     |Yes      |Yes
+|**Other features**  |Cross-platform         |Yes     |Partly         |Partly       |Yes    |Yes      |Yes
+|                    |Reading STDIN          |Yes     |Yes            |Yes          |--     |Yes      |Yes
+|                    |Reading gzipped file   |Yes     |Yes            |--           |--     |Yes      |Yes
+|                    |Writing gzip file      |Yes     |--             |--           |--     |Yes      |--
+
+**Note 1**: See [version information](http://bioinf.shenwei.me/seqkit/benchmark/#softwares) of the softwares.
+
+**Note 2**: See [usage](http://bioinf.shenwei.me/seqkit/usage/) for detailed options of seqkit.
+
+## Benchmark
+
+More details: [http://bioinf.shenwei.me/seqkit/benchmark/](http://bioinf.shenwei.me/seqkit/benchmark/)
+
+Datasets:
+
+    $ seqkit stat *.fa
+    file          format  type   num_seqs        sum_len  min_len       avg_len      max_len
+    dataset_A.fa  FASTA   DNA      67,748  2,807,643,808       56      41,442.5    5,976,145
+    dataset_B.fa  FASTA   DNA         194  3,099,750,718      970  15,978,096.5  248,956,422
+    dataset_C.fq  FASTQ   DNA   9,186,045    918,604,500      100           100          100
+
+SeqKit version: v0.3.1.1
+
+FASTA:
+
+![benchmark-5tests.tsv.png](benchmark/benchmark.5tests.tsv.png)
+
+FASTQ:
+
+![benchmark-5tests.tsv.png](benchmark/benchmark.5tests.tsv.C.png)