Convert SAM to Markdown.
Drop a SAM alignment and get a readable Markdown summary in seconds. It runs entirely in your browser, so your file never leaves your device.
Drag & drop your files
or
Optimize for AI & RAG
Extra cleanup for LLM ingestion: strip HTML, fix smart quotes, tidy Unicode and spacing.
Add YAML front matter
Prepend a metadata block (title, source, date, word & token counts) for knowledge bases and RAG.
Add table of contents
Build a linked index from the headings. Handy for long documents.
Export RAG chunks (.json)
Split the result into retrieval-ready chunks. Download per file from the result panel.
Most converters quietly upload your documents to a server. This one physically can't.
Built for tools,
not for reading.
A SAM file packs every read onto one dense tab-separated line, with header lines, flags and CIGAR strings built for aligners. Converting pulls out the counts and the key fields as a readable Markdown table.
@HD VN:1.6 SO:coordinate
@SQ SN:chr1 LN:248956422
read1 0 chr1 100 60 50M
read2 16 chr1 200 60 50M
# Sequence alignment (SAM)
- **Reads:** 2
- **Reference sequences:** 1
| QNAME | FLAG | RNAME | POS | MAPQ | CIGAR |
| --- | --- | --- | --- | --- | --- |
| read1 | 0 | chr1 | 100 | 60 | 50M |
| read2 | 16 | chr1 | 200 | 60 | 50M |
Everything you
actually need.
A SAM alignment in, a readable Markdown summary out, with no server and no account anywhere.
It never leaves your browser
Your .sam file is read and parsed on your own device. Nothing is uploaded to any server, ever.
# Heading
- point one
3 chunks
AI & RAG ready
Optional cleanup, YAML front matter, a table of contents and RAG chunk export.
Works offline
Once the page has loaded you can switch off your connection and it keeps converting.
Alignments become a table
The read and reference counts head the output, then the first six fields of each read fill a clean pipe table.
Unicode safe
Accents, symbols and non-Latin scripts come through intact as UTF-8.
Free, and unlimited
No sign-up, no quotas, no watermarks. Convert one file or a thousand; it all runs the same way, on your own device.
What survives
the trip.
Honest about what comes through, and what doesn't. These are the same notes the Formats list shows for SAM, so the page never drifts from what the converter really does.
Kept
2- Read and reference-sequence counts
- A table of the first six fields for up to 200 reads
Dropped
4- The sequence
- The quality scores
- Optional tags
- Rows beyond 200
SEQ: ACGTACGTACGTACGTACGT...
QUAL: IIIIIIIIIIIIIIIIIIII...
NM:i:0 MD:Z:50 AS:i:0
SAM questions,
answered.
Everything worth knowing before you drop in a SAM file.
Other converters.
Working with more than SAM files? These convert the same way: privately, in your browser.
INI / config to Markdown
.ini · .conf · .cfg
Classic key-value config.
Environment to Markdown
.env
Environment variable files.
KDL to Markdown
.kdl
KDL document language.
LDIF to Markdown
.ldif
LDAP directory records.
OpenAPI / Swagger to Markdown
.json · .yaml
REST API specifications.
RAML to Markdown
.raml
RESTful API modeling language.
API Blueprint to Markdown
.apib
API Blueprint specifications.
WSDL to Markdown
.wsdl
SOAP web-service definitions.