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lines changed Original file line number Diff line number Diff line change @@ -9,13 +9,7 @@ files from DNA sequencing machines, commonly used in Sanger capillary sequencing
99
1010- [ ** API reference** ] ( https://quadram-institute-bioscience.github.io/nim-abif/ )
1111
12- ## Features
13-
14- - Parse ` .ab1 ` and ` .fsa ` trace files
15- - Extract sequence data, quality values, and sample names
16- - Supports all standard ABIF data types
17- - Export to FASTA and FASTQ formats
18- - Correctly handles big-endian binary data
12+
1913
2014## Installation
2115
@@ -69,13 +63,9 @@ let rawData = trace.getData("DATA1") # Raw channel data
6963
7064The library provides three command-line tools:
7165
72- #### Basic FASTA export
66+
7367
74- ```
75- abif trace.ab1 output.fa
76- ```
77-
78- #### Advanced FASTQ converter with quality trimming
68+ #### FASTQ converter with quality trimming
7969
8070```
8171abi2fq trace.ab1 output.fq
@@ -108,6 +98,16 @@ abimerge --pct-id=90 fwd.ab1 rev.ab1 # Require 90% identity in overlap regio
10898abimerge --verbose fwd.ab1 rev.ab1 # Show alignment details
10999```
110100
101+ #### Render traces
102+
103+ Convert a trace (or part of it) into SVG
104+
105+ ![ rendered chromas] ( docs/chromas.png )
106+
107+ ``` bash
108+ abichromatogram tests/A_forward.ab1 -o A.svg -s 500 -e 1000 --width 1600
109+ ```
110+
111111## Data Types
112112
113113The ABIF format supports various data types, all of which are properly handled by this parser:
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