bam-files

ding-lab/msisensor

microsatellite instability detection using tumor only or paired tumor-normal data

davetang/learning_bam_file

Learning the Sequence Alignment/Map format

nsalomonis/altanalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

slowkow/pytabix

:card_index: Retrieve data in genomic intervals with a Python interface for tabix.

BioJulia/BioAlignments.jl

Sequence alignment tools

IARCbioinfo/needlestack

Multi-sample somatic variant caller

telatin/covtobed

⛰ covtobed | Convert the coverage track from a BAM file into a BED file

pbenner/gonetics

Go / Golang Bioinformatics Library

slowkow/picardmetrics

:vertical_traffic_light: Run Picard on BAM files and collate 90 metrics into one file.

EI-CoreBioinformatics/portcullis

Splice junction analysis and filtering from BAM files

jonas-fuchs/BAMdash

create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks

BioJulia/XAM.jl

Parse and process SAM and BAM formatted files

zhpn1024/ribotish

Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data

PoisonAlien/somaticfreq

knowledge-based genotyping of cancer hotspots from the tumor BAM files

USDA-VS/vSNP

vSNP -- validate SNPs

chgibb/PHAT

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

luntergroup/bamsplit

Split a BAM file by haplotype support

ANGSD-wrapper/angsd-wrapper

Utilities for analyzing next generation sequencing data.

BioJulia/ReadDatastores.jl

Datastores for reads, not your papa's FASTQ files.

biodata-fun/htslib_howto

Collection of simple C scripts for parsing vcf or bam files using the htslib C library. These scripts can be used as the starting point for more complex scripts

jslfree080/bamscope

A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)

wtsi-npg/bambi

Process Illumina instrument data into SAM/BAM/CRAM files.

mnievesc/Ancient_mtDNA_Pipeline

Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.

DKFZ-ODCF/AlignmentAndQCWorkflows

The DKFZ alignment workflow plugin originally developed at the eilslabs

harper357/bam_spot_check

A Python3 script to quickly spot check 10 random sequences from a BAM/FASTx file.

mpieva/biohazard-tools

Udo Stenzel's biohazard-tools — a collection of command-line utilities for bioinformatics [MIRROR]

wckdouglas/sequencing_tools

A python package storing different tools for different NGS operations

Arkanosis/bamrescue

Utility to check Binary Sequence Alignment / Map (BAM) files for corruption and repair them

swyder/Genomic_Utilities

USDA-VS/vSNP3

vSNP -- validate SNPs

DoubleHelixApp/DoubleHelix

Genomic data manipulation tool

DKFZ-ODCF/nf-bam2fastq

Nextflow-based BAM-to-FASTQ conversion and FASTQ-sorting workflow.

IARCbioinfo/addreplacerg-nf

Apply samtools addreplacerg to add a new read group and assign all reads to it in a BAM file

ionCRAM/ionCRAM

https://ioncram.saudigenomeproject.com/

pcantalupo/bam2circos

Visualize your BAM alignments with Circos