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• BamUtil
  Programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam. Tools to Rewrite SAM/BAM Files:
  3 KB (328 words) - 18:02, 12 August 2022
• Samtools
  ...ts. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a
  3 KB (357 words) - 22:04, 21 August 2022
• Samblaster
  ...onally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file.
  2 KB (296 words) - 22:03, 21 August 2022
• ElPrep
  ...y advantage of elPrep is that it only performs a single-pass to process a .sam/.bam file, independent of the number of processing steps that need to be ap
  3 KB (345 words) - 21:20, 6 December 2019
• Picard-tools
  ...rmat is a generic format for storing large nucleotide sequence alignments. SAM is described in the SAMtools project page. ...ating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.
  6 KB (882 words) - 15:25, 27 January 2023
• SAMStat
  ...stq and after mapping to a reference genome in the alignment / map format (SAM/BAM). To monitor the sequence quality over time and to identify problems it ...e sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately m
  3 KB (429 words) - 20:34, 12 August 2022
• Ea-utils
  : sam-stats :: Basic sam/bam stats. Like other tools, but produces what I want to look at, in a form
  4 KB (438 words) - 14:54, 15 August 2022
• Samapi
  A web API for SAM implemented with FastAPI.
  2 KB (241 words) - 16:57, 19 August 2024
• Pysamstats
  ...le statistics against genome positions based on sequence alignments from a SAM or BAM file.
  2 KB (259 words) - 19:52, 29 September 2020
• SNPsplit
  ...ele-specific alignment sorter which is designed to read alignment files in SAM/ BAM format and determine the allelic origin of reads that cover known SNP
  2 KB (282 words) - 20:38, 27 May 2022
• OCOCO
  ...online consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
  2 KB (284 words) - 21:22, 6 December 2019
• Sambamba
  Sambamba is a high performance modern robust and fast tool for working with SAM and BAM files. Sambamba is written in the D programming language and becaus
  2 KB (299 words) - 20:33, 12 August 2022
• Resistome
  ...e resistome of large metagenomic dataets. This program takes in as input a SAM formatted alignment file, a FASTA formatted reference database, and a CSV f
  2 KB (297 words) - 21:46, 21 August 2022
• HAPCUT
  ...om next-generation sequencing platforms. HapCUT takes as input the aligned SAM/BAM files for an individual diploid genome and the list of variants, and ou
  2 KB (298 words) - 18:13, 15 August 2022
• Fairseq
  ...Modeling. Myle Ott and Sergey Edunov and Alexei Baevski and Angela Fan and Sam Gross and Nathan Ng and David Grangier and Michael Auli. Proceedings of NAA
  3 KB (296 words) - 15:18, 15 August 2022
• Wise
  ...arson). There are other packages, such as the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused on hidden Markov models (HMMs) of biopolyme
  3 KB (321 words) - 21:29, 6 December 2019
• Sniffles
  ...output from BWA-MEM (use -M and -x parameter) or NGM-LR with the optional SAM attributes enabled!
  3 KB (305 words) - 00:03, 22 August 2022
• Salmon
  ...tionally, Salmon can make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads.
  3 KB (305 words) - 19:29, 3 June 2022
• Bioawk
  ...ral common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a f
  3 KB (308 words) - 12:54, 15 August 2022
• ContaVect
  ...mologies masking, fastq filtering/adapter trimming, short read alignments, SAM file splitting and generating human readable output.
  3 KB (309 words) - 20:40, 10 June 2022

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