diamond by bbuchfink

Accelerated BLAST compatible local sequence aligner.

updated at April 25, 2024, 9:47 p.m.

37 +0

958 +4

169 -1

SnpEff by pcingola

None

updated at April 25, 2024, 7:34 p.m.

24 +0

228 +1

74 +0

bwa by lh3

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

updated at April 25, 2024, 6:27 p.m.

107 +1

1,453 +10

544 +2

zindex by mattgodbolt

Create an index on a compressed text file

updated at April 25, 2024, 3:47 p.m.

23 +0

614 +1

41 +0

cufflinks by cole-trapnell-lab

None

updated at April 25, 2024, 3:01 p.m.

36 +0

301 +1

115 +0

pyfaidx by mdshw5

Efficient pythonic random access to fasta subsequences

updated at April 25, 2024, 2:33 p.m.

9 +0

440 +0

73 +0

pyensembl by openvax

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

updated at April 25, 2024, 1:45 p.m.

22 +0

352 +0

66 +0

FastQC by s-andrews

A quality control analysis tool for high throughput sequencing data

updated at April 25, 2024, 12:37 p.m.

12 +0

388 +2

79 +0

Flye by fenderglass

De novo assembler for single molecule sequencing reads using repeat graphs

updated at April 25, 2024, 11:54 a.m.

28 +0

726 +1

160 +1

poly by bebop

A Go package for engineering organisms.

updated at April 25, 2024, 8:23 a.m.

12 +0

649 +1

68 +0

seqtk by lh3

Toolkit for processing sequences in FASTA/Q formats

updated at April 25, 2024, 6:08 a.m.

62 +0

1,312 +2

307 +1

parasail by jeffdaily

Pairwise Sequence Alignment Library

updated at April 25, 2024, 5:52 a.m.

18 +0

233 +1

34 +0

cromwell by broadinstitute

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

updated at April 24, 2024, 3:26 p.m.

112 -1

958 +1

349 +1

WFA2-lib by smarco

WFA-lib: Wavefront alignment algorithm library v2

updated at April 24, 2024, 4:32 a.m.

13 +0

142 +3

29 +0

pysam by pysam-developers

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

updated at April 24, 2024, 2:55 a.m.

48 +0

749 -1

270 +1

rnaseq_tutorial by griffithlab

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

updated at April 23, 2024, 9:53 p.m.

184 +0

1,310 +0

615 +0

lumpy-sv by arq5x

lumpy: a general probabilistic framework for structural variant discovery

updated at April 23, 2024, 8:49 p.m.

27 +0

299 +1

118 +0

cruzdb by brentp

python access to UCSC genomes database

updated at April 23, 2024, 8:01 p.m.

17 +0

134 +1

41 +0

gffutils by daler

GFF and GTF file manipulation and interconversion

updated at April 23, 2024, 3:10 p.m.

14 +0

267 +2

74 +0

AGAT by NBISweden

Another Gtf/Gff Analysis Toolkit

updated at April 23, 2024, 2:20 p.m.

46 +0

409 +4

52 -1