Nils Homer

Nils Homer

Bioinformatics Tools Series

Bioinformatic Tool Series: SAM to FASTQ with UMIs and Barcodes

December 14, 2017Bioinformatics, Bioinformatics Tools Series No Comments

This continues the series of posts meant to help you write concise and well-tested bioinformatic tools. Today I’ll briefly describe a tool named SamToFastq that converts a SAM (or BAM) to FASTQ, when the SAM has bases and qualities stored in auxiliary tags that need to be included in the FASTQs bases and qualities. This … Read More

Bioinformatics Tools Series: Logging and Progress Logging

November 20, 2017Bioinformatics, Bioinformatics Tools Series No Comments

This continues the series of posts meant to help you write concise and well-tested bioinformatic tools. We previously wrote a tool to ensure that the NM/UQ/MD SAM tags on each read are accurate.  Lets add some logging information to the tool, to print out the input and output SAM or BAM file paths, and report some progress … Read More

Bioinformatics Tools Series: Writing a SAM or BAM file

November 13, 2017Bioinformatics, Bioinformatics Tools Series No Comments

This continues the series of posts meant to help you write concise and well-tested bioinformatic tools. Lets write a tool that reads a BAM file, does some modification to the records, then writes a BAM file. Lets ensure that the NM/UQ/MD SAM tags on each read are accurate, which is important if aligners aren’t well-behaved … Read More

Bioinformatics Tools Series: Reading a SAM or BAM file

November 7, 2017Bioinformatics, Bioinformatics Tools Series No Comments

This continues the series of posts meant to help you write concise and well-tested bioinformatic tools. Lets write a tool that reads a SAM or a BAM file.  Since just reading it is boring, lets count the number of fragment and paired end reads respectively.  Here’s the tool: Lets examine it in a little more … Read More

Bioinformatics Tools Series: SAM Optional Tags

November 6, 2017Bioinformatics, Bioinformatics Tools Series No Comments

This continues the series of posts meant to help you write concise and well-tested bioinformatic tools. One common thing to do is to retrieve, set, or update the SAM optional tags on each SAM record.  The SAM optional fields (tags) specification lists predefined standard tags, though users can add their own (start with a X, Y, … Read More

Building Concise and Well-Tested Bioinformatic Tools

November 4, 2017Bioinformatics, Bioinformatics Tools Series No Comments

This is the start of a series of posts introducing various ways of implementing cohesive, concise, and well-tested bioinformatic tools in scala using many of the APIs found in fgbio (see the latest scaladoc, list of tools, and list of metrics).  Each post will be build on each other to help familiarize folks with how I build simple … Read More

Recent Posts

  • DemuxFastqs with multiple FASTQs per Read
  • Bioinformatic Tool Series: SAM to FASTQ with UMIs and Barcodes
  • Bioinformatics Tools Series: Logging and Progress Logging
  • Bioinformatics Tools Series: Writing a SAM or BAM file
  • Bioinformatics Tools Series: Reading a SAM or BAM file

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