Skip to content

Commit

Permalink
[DOC] Update README badges
Browse files Browse the repository at this point in the history
  • Loading branch information
eseiler committed Sep 27, 2024
1 parent a51bb3d commit 53c3cd1
Showing 1 changed file with 8 additions and 3 deletions.
11 changes: 8 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,8 +1,13 @@
## Needle
## Needle [![build status][1]][2] [![codecov][3]][4] [![install with bioconda][5]][6]

### A fast and space-efficient pre-filter for estimating the quantification of very large collections of nucleotide sequences
[1]: https://img.shields.io/github/actions/workflow/status/seqan/needle/ci_linux.yml?branch=main&style=flat&logo=github&label=CI "Open GitHub actions page"
[2]: https://github.com/seqan/needle/actions?query=branch%3Amain
[3]: https://codecov.io/gh/seqan/needle/graph/badge.svg?token=W109QS58E0 "Open Codecov page"
[4]: https://codecov.io/gh/seqan/needle
[5]: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
[6]: #install-with-bioconda-linux

[![Build Status](https://github.com/seqan/app-template/workflows/App%20CI/badge.svg)](https://github.com/seqan/needle/actions?query=branch%3Amaster+workflow%3A%22App+CI%22) [![codecov](https://codecov.io/gh/seqan/needle/branch/master/graph/badge.svg?token=SJVMYRUKW2)](https://codecov.io/gh/seqan/needle) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](#install-with-bioconda-linux)
### A fast and space-efficient pre-filter for estimating the quantification of very large collections of nucleotide sequences

Needle is a tool for semi-quantitative analysis of very large collections of nucleotide sequences.
Needle stores its data in multiple interleaved Bloom filter, a fast and space efficient probabilistic data structure and uses a windowing scheme (also called minimisers) to reduce the amount of data to store. How many interleaved Bloom filter are used is defined by the user. Each interleaved Bloom filter has a so called expression threshold and stores minimisers with an occurrence greater than or equal to its own expression threshold and smaller than the next biggest expression threshold (if there is no bigger expression threshold, all greater than or equal to the threshold are stored). These expression thresholds are then used during the query (called estimate) to approximate the expression values of given transcripts.
Expand Down

0 comments on commit 53c3cd1

Please sign in to comment.