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50 public repositories
matching this topic...
microsatellite instability detection using tumor only or paired tumor-normal data
Learning the Sequence Alignment/Map format
Updated
Mar 13, 2022
Perl
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.
Updated
Sep 4, 2021
Python
📇 Retrieve data in genomic intervals with a Python interface for tabix.
Updated
Feb 15, 2022
Julia
Multi-sample somatic variant caller
🚦 Run Picard on BAM files and collate 90 metrics into one file.
Updated
Sep 27, 2017
Shell
⛰ covtobed | Convert the coverage track from a BAM file into a BED file
Go / Golang Bioinformatics Library
Splice junction analysis and filtering from BAM files
Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
Updated
Feb 11, 2022
TypeScript
Utilities for analyzing next generation sequencing data.
Updated
May 7, 2021
Shell
Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data
Updated
Jul 2, 2021
Python
Updated
Feb 14, 2020
Python
Split a BAM file by haplotype support
Updated
Dec 13, 2017
Python
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
knowledge-based genotyping of cancer hotspots from the tumor BAM files
Process Illumina instrument data into SAM/BAM/CRAM files.
A Python3 script to quickly spot check 10 random sequences from a BAM/FASTx file.
Updated
Feb 19, 2018
Python
Datastores for reads, not your papa's FASTQ files.
Updated
Jun 7, 2020
Julia
A python package storing different tools for different NGS operations
Updated
Sep 13, 2021
HTML
Udo Stenzel's biohazard-tools — a collection of command-line utilities for bioinformatics [MIRROR]
Updated
Mar 18, 2021
Haskell
Utility to check Binary Sequence Alignment / Map (BAM) files for corruption and repair them
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
Updated
Mar 27, 2020
Shell
The DKFZ alignment workflow plugin originally developed at the eilslabs.
Updated
Mar 17, 2022
Python
Visualize your BAM alignments with Circos
Updated
Jun 27, 2017
Perl
FLiCK - Format LeveragIng Compression frameworK
Updated
Dec 22, 2017
Java
Nextflow-based BAM-to-FASTQ conversion and FASTQ-sorting workflow.
Updated
Feb 9, 2022
Shell
Apply samtools addreplacerg to add a new read group and assign all reads to it in a BAM file
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Make
seqnamean alias ofrefnameto makeseqnameconsistent with the rest of the BioJulia ecosystem - namely GenomicFeatures.