mergesam by DarwinAwardWinner

Automate common sam & bam conversions

updated at Jan. 6, 2016, 2:02 a.m.

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bam-toolbox by AndersenLab

A bam toolbox

updated at March 4, 2020, 12:06 a.m.

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ruffus by cgat-developers

CGAT-ruffus is a lightweight python module for running computational pipelines

updated at Dec. 15, 2023, 2:59 a.m.

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cyvcf by arq5x

A fast Python library for VCF files leveraging Cython for speed.

updated at Jan. 22, 2024, 10:32 a.m.

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bioservices by cokelaer

Access to Biological Web Services from Python.

updated at March 4, 2024, 8 p.m.

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easy_qsub by shenwei356

Easily submitting multiple PBS jobs or running local jobs in parallel. Multiple input files supported.

updated at March 13, 2024, 5:58 a.m.

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smof by incertae-sedis

Explore and analyze biological sequence data

updated at March 17, 2024, 5:55 p.m.

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fastqp by mdshw5

Simple FASTQ quality assessment using Python

updated at March 25, 2024, 9:06 a.m.

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AfterQC by OpenGene

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

updated at March 26, 2024, 7:30 a.m.

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squiggle by IQTLabs

📈 DNA Sequence Visualization for Humans

updated at March 27, 2024, 4:50 a.m.

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seqmagick by fhcrc

An imagemagick-like frontend to Biopython SeqIO

updated at March 31, 2024, 9:30 p.m.

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wormtable by wormtable

Write-once-read-many table for large datasets.

updated at April 5, 2024, 5:59 p.m.

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PyVCF by jamescasbon

A Variant Call Format reader for Python.

updated at April 10, 2024, 9:48 a.m.

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pybedtools by daler

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

updated at April 11, 2024, 12:51 a.m.

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ggd-cli by gogetdata

The command-line interface to GGD

updated at April 17, 2024, 12:59 p.m.

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poapy by ljdursi

A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes

updated at April 18, 2024, 7:29 p.m.

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bcbio-nextgen by bcbio

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

updated at April 22, 2024, 11:12 a.m.

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deepvariant by google

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

updated at April 22, 2024, 11:23 p.m.

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bamsurgeon by adamewing

tools for adding mutations to existing .bam files, used for testing mutation callers

updated at April 23, 2024, 8:44 a.m.

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redun by insitro

Yet another redundant workflow engine

updated at April 23, 2024, 9:54 a.m.

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