Skip to content

Commit

Permalink
update doc
Browse files Browse the repository at this point in the history
  • Loading branch information
@shenwei356
shenwei356 committed Jan 31, 2024
1 parent 09ca7ab commit 9e3445a
Show file tree
Hide file tree
Showing 5 changed files with 85 additions and 32 deletions.
12 changes: 6 additions & 6 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -53,12 +53,11 @@ install via conda:
| |[faidx](https://bioinf.shenwei.me/seqkit/usage/#faidx) |Create the FASTA index file and extract subsequences (with more features than samtools faidx)|FASTA |+ or/and - | |
| |[translate](https://bioinf.shenwei.me/seqkit/usage/#translate) |translate DNA/RNA to protein sequence |FASTA/Q |+ or/and - | |
| |[watch ](https://bioinf.shenwei.me/seqkit/usage/#watch ) |Monitoring and online histograms of sequence features |FASTA/Q | | |
| |[sana](https://bioinf.shenwei.me/seqkit/usage/#sana) |Sanitize broken single line FASTQ files |FASTQ | | |
| |[scat ](https://bioinf.shenwei.me/seqkit/usage/#scat ) |Real time concatenation and streaming of fastx files |FASTA/Q | |✓ |
|Format conversion|[fq2fa](https://bioinf.shenwei.me/seqkit/usage/#fq2fa) |Convert FASTQ to FASTA format |FASTQ | | |
| |[fx2tab](https://bioinf.shenwei.me/seqkit/usage/#fx2tab) |Convert FASTA/Q to tabular format |FASTA/Q | | |
| |[fa2fq](https://bioinf.shenwei.me/seqkit/usage/#fa2fq) |Retrieve corresponding FASTQ records by a FASTA file |FASTA/Q |+ only | |
| |[tab2fx](https://bioinf.shenwei.me/seqkit/usage/#tab2fx) |Convert tabular format to FASTA/Q format |FASTA/Q | | |
| |[tab2fx](https://bioinf.shenwei.me/seqkit/usage/#tab2fx) |Convert tabular format to FASTA/Q format |TSV | | |
| |[convert](https://bioinf.shenwei.me/seqkit/usage/#convert) |Convert FASTQ quality encoding between Sanger, Solexa and Illumina |FASTA/Q | | |
|Searching |[grep](https://bioinf.shenwei.me/seqkit/usage/#grep) |Search sequences by ID/name/sequence/sequence motifs, mismatch allowed |FASTA/Q |+ and - |partly, -m |
| |[locate](https://bioinf.shenwei.me/seqkit/usage/#locate) |Locate subsequences/motifs, mismatch allowed |FASTA/Q |+ and - |partly, -m |
Expand All @@ -74,16 +73,17 @@ install via conda:
| |[head-genome](https://bioinf.shenwei.me/seqkit/usage/#head-genome) |Print sequences of the first genome with common prefixes in name |FASTA/Q | | |
| |[range](https://bioinf.shenwei.me/seqkit/usage/#range) |Print FASTA/Q records in a range (start:end) |FASTA/Q | | |
| |[pair](https://bioinf.shenwei.me/seqkit/usage/#pair) |Patch up paired-end reads from two fastq files |FASTA/Q | | |
|Edit |[concat](https://bioinf.shenwei.me/seqkit/usage/#concat) |Concatenate sequences with same ID from multiple files |FASTA/Q |+ only | |
| |[replace](https://bioinf.shenwei.me/seqkit/usage/#replace) |Replace name/sequence by regular expression |FASTA/Q |+ only | |
|Edit |[replace](https://bioinf.shenwei.me/seqkit/usage/#replace) |Replace name/sequence by regular expression |FASTA/Q |+ only | |
| |[rename](https://bioinf.shenwei.me/seqkit/usage/#rename) |Rename duplicated IDs |FASTA/Q | | |
| |[concat](https://bioinf.shenwei.me/seqkit/usage/#concat) |Concatenate sequences with same ID from multiple files |FASTA/Q |+ only | |
| |[restart](https://bioinf.shenwei.me/seqkit/usage/#restart) |Reset start position for circular genome |FASTA/Q |+ only | |
| |[mutate](https://bioinf.shenwei.me/seqkit/usage/#mutate) |Edit sequence (point mutation, insertion, deletion) |FASTA/Q |+ only | |
| |[rename](https://bioinf.shenwei.me/seqkit/usage/#rename) |Rename duplicated IDs |FASTA/Q | | |
| |[sana](https://bioinf.shenwei.me/seqkit/usage/#sana) |Sanitize broken single line FASTQ files |FASTQ | | |
|Ordering |[sort](https://bioinf.shenwei.me/seqkit/usage/#sort) |Sort sequences by id/name/sequence/length |FASTA preffered| | |
| |[shuffle](https://bioinf.shenwei.me/seqkit/usage/#shuffle) |Shuffle sequences |FASTA preffered| | |
|BAM processing |[bam](https://bioinf.shenwei.me/seqkit/usage/#bam) |Monitoring and online histograms of BAM record features |BAM | | |
|Miscellaneous |[sum](https://bioinf.shenwei.me/seqkit/usage/#sum) |Compute message digest for all sequences in FASTA/Q files |FASTA/Q | |✓ |
| |[merge-slides](https://bioinf.shenwei.me/seqkit/usage/#merge-slides)|Merge sliding windows generated from seqkit sliding |text | | |
| |[merge-slides](https://bioinf.shenwei.me/seqkit/usage/#merge-slides)|Merge sliding windows generated from seqkit sliding |TSV | |

Notes:

Expand Down
12 changes: 6 additions & 6 deletions doc/docs/commands.csv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,11 @@ Basic operation,[seq](https://bioinf.shenwei.me/seqkit/usage/#seq),"Transform se
,[faidx](https://bioinf.shenwei.me/seqkit/usage/#faidx),Create the FASTA index file and extract subsequences (with more features than samtools faidx),FASTA,+ or/and -,
,[translate](https://bioinf.shenwei.me/seqkit/usage/#translate),translate DNA/RNA to protein sequence,FASTA/Q,+ or/and -,
,[watch ](https://bioinf.shenwei.me/seqkit/usage/#watch ),Monitoring and online histograms of sequence features,FASTA/Q,,
,[sana](https://bioinf.shenwei.me/seqkit/usage/#sana),Sanitize broken single line FASTQ files,FASTQ,,
,[scat ](https://bioinf.shenwei.me/seqkit/usage/#scat ),Real time concatenation and streaming of fastx files,FASTA/Q,,✓
Format conversion,[fq2fa](https://bioinf.shenwei.me/seqkit/usage/#fq2fa),Convert FASTQ to FASTA format,FASTQ,,
,[fx2tab](https://bioinf.shenwei.me/seqkit/usage/#fx2tab),Convert FASTA/Q to tabular format,FASTA/Q,,
,[fa2fq](https://bioinf.shenwei.me/seqkit/usage/#fa2fq),Retrieve corresponding FASTQ records by a FASTA file,FASTA/Q,+ only,
,[tab2fx](https://bioinf.shenwei.me/seqkit/usage/#tab2fx),Convert tabular format to FASTA/Q format,FASTA/Q,,
,[tab2fx](https://bioinf.shenwei.me/seqkit/usage/#tab2fx),Convert tabular format to FASTA/Q format,TSV,,
,[convert](https://bioinf.shenwei.me/seqkit/usage/#convert),"Convert FASTQ quality encoding between Sanger, Solexa and Illumina",FASTA/Q,,
Searching,[grep](https://bioinf.shenwei.me/seqkit/usage/#grep),"Search sequences by ID/name/sequence/sequence motifs, mismatch allowed",FASTA/Q,+ and -,"partly, -m"
,[locate](https://bioinf.shenwei.me/seqkit/usage/#locate),"Locate subsequences/motifs, mismatch allowed",FASTA/Q,+ and -,"partly, -m"
Expand All @@ -27,13 +26,14 @@ Set operation,[sample](https://bioinf.shenwei.me/seqkit/usage/#sample),Sample se
,[head-genome](https://bioinf.shenwei.me/seqkit/usage/#head-genome),Print sequences of the first genome with common prefixes in name,FASTA/Q,,
,[range](https://bioinf.shenwei.me/seqkit/usage/#range),Print FASTA/Q records in a range (start:end),FASTA/Q,,
,[pair](https://bioinf.shenwei.me/seqkit/usage/#pair),Patch up paired-end reads from two fastq files,FASTA/Q,,
Edit,[concat](https://bioinf.shenwei.me/seqkit/usage/#concat),Concatenate sequences with same ID from multiple files,FASTA/Q,+ only,
,[replace](https://bioinf.shenwei.me/seqkit/usage/#replace),Replace name/sequence by regular expression,FASTA/Q,+ only,
Edit,[replace](https://bioinf.shenwei.me/seqkit/usage/#replace),Replace name/sequence by regular expression,FASTA/Q,+ only,
,[rename](https://bioinf.shenwei.me/seqkit/usage/#rename),Rename duplicated IDs,FASTA/Q,,
,[concat](https://bioinf.shenwei.me/seqkit/usage/#concat),Concatenate sequences with same ID from multiple files,FASTA/Q,+ only,
,[restart](https://bioinf.shenwei.me/seqkit/usage/#restart),Reset start position for circular genome,FASTA/Q,+ only,
,[mutate](https://bioinf.shenwei.me/seqkit/usage/#mutate),"Edit sequence (point mutation, insertion, deletion)",FASTA/Q,+ only,
,[rename](https://bioinf.shenwei.me/seqkit/usage/#rename),Rename duplicated IDs,FASTA/Q,,
,[sana](https://bioinf.shenwei.me/seqkit/usage/#sana),Sanitize broken single line FASTQ files,FASTQ,,
Ordering,[sort](https://bioinf.shenwei.me/seqkit/usage/#sort),Sort sequences by id/name/sequence/length,FASTA preffered,,
,[shuffle](https://bioinf.shenwei.me/seqkit/usage/#shuffle),Shuffle sequences,FASTA preffered,,
BAM processing,[bam](https://bioinf.shenwei.me/seqkit/usage/#bam),Monitoring and online histograms of BAM record features,BAM,,
Miscellaneous,[sum](https://bioinf.shenwei.me/seqkit/usage/#sum),Compute message digest for all sequences in FASTA/Q files,FASTA/Q,,✓
,[merge-slides](https://bioinf.shenwei.me/seqkit/usage/#merge-slides),Merge sliding windows generated from seqkit sliding,text,,
,[merge-slides](https://bioinf.shenwei.me/seqkit/usage/#merge-slides),Merge sliding windows generated from seqkit sliding,TSV,,
Loading

0 comments on commit 9e3445a

Please sign in to comment.